Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category. wwPDB recommends wwPDB-assigned residue number, residue ID, and chain ID, _atom_site.auth_seq_id _atom_site.auth_comp_id, and attribute auth_asym_id in category atom_site, respectively, to be used for publication materials. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_siteCategory> <PDBx:atom_site id="1"> <PDBx:B_iso_or_equiv>17.93</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.369</PDBx:Cartn_x> <PDBx:Cartn_y>30.691</PDBx:Cartn_y> <PDBx:Cartn_z>11.795</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="2"> <PDBx:B_iso_or_equiv>17.75</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.970</PDBx:Cartn_x> <PDBx:Cartn_y>31.965</PDBx:Cartn_y> <PDBx:Cartn_z>12.332</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="3"> <PDBx:B_iso_or_equiv>17.83</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.569</PDBx:Cartn_x> <PDBx:Cartn_y>32.010</PDBx:Cartn_y> <PDBx:Cartn_z>13.808</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="4"> <PDBx:B_iso_or_equiv>17.53</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.735</PDBx:Cartn_x> <PDBx:Cartn_y>31.190</PDBx:Cartn_y> <PDBx:Cartn_z>14.167</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="5"> <PDBx:B_iso_or_equiv>17.66</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.379</PDBx:Cartn_x> <PDBx:Cartn_y>33.146</PDBx:Cartn_y> <PDBx:Cartn_z>11.540</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="6"> <PDBx:B_iso_or_equiv>18.86</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.584</PDBx:Cartn_x> <PDBx:Cartn_y>33.034</PDBx:Cartn_y> <PDBx:Cartn_z>10.030</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG1</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="7"> <PDBx:B_iso_or_equiv>17.12</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.933</PDBx:Cartn_x> <PDBx:Cartn_y>33.309</PDBx:Cartn_y> <PDBx:Cartn_z>11.872</PDBx:Cartn_z> <PDBx:auth_seq_id>11</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>11</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="8"> <PDBx:B_iso_or_equiv>18.97</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.095</PDBx:Cartn_x> <PDBx:Cartn_y>32.930</PDBx:Cartn_y> <PDBx:Cartn_z>14.590</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="9"> <PDBx:B_iso_or_equiv>19.80</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>25.734</PDBx:Cartn_x> <PDBx:Cartn_y>32.995</PDBx:Cartn_y> <PDBx:Cartn_z>16.032</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="10"> <PDBx:B_iso_or_equiv>20.92</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.695</PDBx:Cartn_x> <PDBx:Cartn_y>34.106</PDBx:Cartn_y> <PDBx:Cartn_z>16.113</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="11"> <PDBx:B_iso_or_equiv>21.84</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>24.869</PDBx:Cartn_x> <PDBx:Cartn_y>35.118</PDBx:Cartn_y> <PDBx:Cartn_z>15.421</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="12"> <PDBx:B_iso_or_equiv>20.51</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.911</PDBx:Cartn_x> <PDBx:Cartn_y>33.346</PDBx:Cartn_y> <PDBx:Cartn_z>17.018</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="13"> <PDBx:B_iso_or_equiv>20.29</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.946</PDBx:Cartn_x> <PDBx:Cartn_y>33.921</PDBx:Cartn_y> <PDBx:Cartn_z>16.183</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>3</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>OG1</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="14"> <PDBx:B_iso_or_equiv>20.59</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.769</PDBx:Cartn_x> <PDBx:Cartn_y>32.142</PDBx:Cartn_y> <PDBx:Cartn_z>17.103</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>4</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>OG1</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="15"> <PDBx:B_iso_or_equiv>20.47</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>27.418</PDBx:Cartn_x> <PDBx:Cartn_y>32.181</PDBx:Cartn_y> <PDBx:Cartn_z>17.878</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>3</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="16"> <PDBx:B_iso_or_equiv>20.00</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>26.489</PDBx:Cartn_x> <PDBx:Cartn_y>33.778</PDBx:Cartn_y> <PDBx:Cartn_z>18.426</PDBx:Cartn_z> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:footnote_id>4</PDBx:footnote_id> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id>4</PDBx:label_alt_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>THR</PDBx:label_comp_id> <PDBx:label_seq_id>12</PDBx:label_seq_id> <PDBx:occupancy>0.50</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="17"> <PDBx:B_iso_or_equiv>22.08</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.664</PDBx:Cartn_x> <PDBx:Cartn_y>33.855</PDBx:Cartn_y> <PDBx:Cartn_z>16.884</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>N</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="18"> <PDBx:B_iso_or_equiv>23.44</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>22.623</PDBx:Cartn_x> <PDBx:Cartn_y>34.850</PDBx:Cartn_y> <PDBx:Cartn_z>17.093</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CA</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="19"> <PDBx:B_iso_or_equiv>25.77</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>22.657</PDBx:Cartn_x> <PDBx:Cartn_y>35.113</PDBx:Cartn_y> <PDBx:Cartn_z>18.610</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>C</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="20"> <PDBx:B_iso_or_equiv>26.28</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>23.123</PDBx:Cartn_x> <PDBx:Cartn_y>34.250</PDBx:Cartn_y> <PDBx:Cartn_z>19.406</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>O</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="21"> <PDBx:B_iso_or_equiv>22.67</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>21.236</PDBx:Cartn_x> <PDBx:Cartn_y>34.463</PDBx:Cartn_y> <PDBx:Cartn_z>16.492</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CB</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="22"> <PDBx:B_iso_or_equiv>22.14</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>20.478</PDBx:Cartn_x> <PDBx:Cartn_y>33.469</PDBx:Cartn_y> <PDBx:Cartn_z>17.371</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG1</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="23"> <PDBx:B_iso_or_equiv>21.75</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>21.357</PDBx:Cartn_x> <PDBx:Cartn_y>33.986</PDBx:Cartn_y> <PDBx:Cartn_z>15.016</PDBx:Cartn_z> <PDBx:auth_seq_id>13</PDBx:auth_seq_id> <PDBx:footnote_id xsi:nil="true" /> <PDBx:group_PDB>ATOM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_atom_id>CG2</PDBx:label_atom_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>13</PDBx:label_seq_id> <PDBx:occupancy>1.00</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="101"> <PDBx:B_iso_or_equiv>17.27</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.171</PDBx:Cartn_x> <PDBx:Cartn_y>29.012</PDBx:Cartn_y> <PDBx:Cartn_z>7.116</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>C1</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="102"> <PDBx:B_iso_or_equiv>16.95</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.949</PDBx:Cartn_x> <PDBx:Cartn_y>27.758</PDBx:Cartn_y> <PDBx:Cartn_z>6.793</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>C2</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="103"> <PDBx:B_iso_or_equiv>16.85</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>4.800</PDBx:Cartn_x> <PDBx:Cartn_y>26.678</PDBx:Cartn_y> <PDBx:Cartn_z>7.393</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>O3</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site> <PDBx:atom_site id="104"> <PDBx:B_iso_or_equiv>16.43</PDBx:B_iso_or_equiv> <PDBx:Cartn_x>5.930</PDBx:Cartn_x> <PDBx:Cartn_y>27.841</PDBx:Cartn_y> <PDBx:Cartn_z>5.869</PDBx:Cartn_z> <PDBx:auth_seq_id>300</PDBx:auth_seq_id> <PDBx:footnote_id>1</PDBx:footnote_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id>1</PDBx:label_alt_id> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>N4</PDBx:label_atom_id> <PDBx:label_comp_id>APS</PDBx:label_comp_id> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:occupancy>0.58</PDBx:occupancy> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site> </PDBx:atom_siteCategory> Equivalent isotropic atomic displacement parameter, B~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. B~eq~ = (B~i~ B~j~ B~k~)^1/3^ B~n~ = the principal components of the orthogonalized B^ij^ The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute B_equiv_geom_mean in category atom_site. Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, B~eq~, calculated from the anisotropic displacement parameters. B~eq~ = (1/3) sum~i~[sum~j~(B^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths B^ij^ = 8 pi^2^ U^ij^ Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. Note - The particular type of ADP stored in this item is qualified by item attribute pdbx_adp_type. in category refine The standard uncertainty (estimated standard deviation) of attribute B_iso_or_equiv in category atom_site. The x atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The standard uncertainty (estimated standard deviation) of attribute Cartn_x in category atom_site. The y atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The standard uncertainty (estimated standard deviation) of attribute Cartn_y in category atom_site. The z atom-site coordinate in angstroms specified according to a set of orthogonal Cartesian axes related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The standard uncertainty (estimated standard deviation) of attribute Cartn_z in category atom_site. Equivalent isotropic atomic displacement parameter, U~eq~, in angstroms squared, calculated as the geometric mean of the anisotropic atomic displacement parameters. U~eq~ = (U~i~ U~j~ U~k~)^1/3^ U~n~ = the principal components of the orthogonalized U^ij^ The standard uncertainty (estimated standard deviation) of attribute U_equiv_geom_mean in category atom_site. Isotropic atomic displacement parameter, or equivalent isotropic atomic displacement parameter, U~eq~, calculated from anisotropic atomic displacement parameters. U~eq~ = (1/3) sum~i~[sum~j~(U^ij^ A~i~ A~j~ a*~i~ a*~j~)] A = the real space cell lengths a* = the reciprocal space cell lengths Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. The standard uncertainty (estimated standard deviation) of attribute U_iso_or_equiv in category atom_site. The Wyckoff symbol (letter) as listed in the space-group tables of International Tables for Crystallography, Vol. A (2002). A standard code used to describe the type of atomic displacement parameters used for the site. The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][1] in category atom_site. The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][2] in category atom_site. The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute aniso_B[1][3] in category atom_site. The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute aniso_B[2][2] in category atom_site. The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute aniso_B[2][3] in category atom_site. The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute aniso_B[3][3] in category atom_site. The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][1] in category atom_site. The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][2] in category atom_site. The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute aniso_U[1][3] in category atom_site. The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute aniso_U[2][2] in category atom_site. The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute aniso_U[2][3] in category atom_site. The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute aniso_U[3][3] in category atom_site. Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. The number of hydrogen atoms attached to the atom at this site excluding any hydrogen atoms for which coordinates (measured or calculated) are given. water oxygen 2 hydroxyl oxygen 1 ammonium nitrogen 4 An alternative identifier for attribute label_asym_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. An alternative identifier for attribute label_atom_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. An alternative identifier for attribute label_comp_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. An alternative identifier for attribute label_seq_id in category atom_site that may be provided by an author in order to match the identification used in the publication that describes the structure. Note that this is not necessarily a number, that the values do not have to be positive, and that the value does not have to correspond to the value of attribute label_seq_id in category atom_site. The value of attribute label_seq_id in category atom_site is required to be a sequential list of positive integers. The author may assign values to attribute auth_seq_id in category atom_site in any desired way. For instance, the values may be used to relate this structure to a numbering scheme in a homologous structure, including sequence gaps or insertion codes. Alternatively, a scheme may be used for a truncated polymer that maintains the numbering scheme of the full length polymer. In all cases, the scheme used here must match the scheme used in the publication that describes the structure. The attribute id in category atom_site of the atom site to which the 'geometry-calculated' atom site is attached. A standard code to signal whether the site coordinates have been determined from the intensities or calculated from the geometry of surrounding sites, or have been assigned dummy values. The abbreviation 'c' may be used in place of 'calc'. This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. A description of the constraints applied to parameters at this site during refinement. See also attribute refinement_flags in category atom_site and attribute ls_number_constraints in category refine. pop=1.0-pop(Zn3) A description of special aspects of this site. See also attribute refinement_flags in category atom_site. Ag/Si disordered A code which identifies a cluster of atoms that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, attribute disorder_group in category atom_site is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order. *** This data item would not in general be used in a macromolecular data block. *** A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not. A minus prefix (e.g. '-1') is used to indicate sites disordered about a special position. *** This data item would not in general be used in a macromolecular data block. *** The value of attribute footnote_id in category atom_site must match an ID specified by attribute id in category atom_sites_footnote in the ATOM_SITES_FOOTNOTE list. The x coordinate of the atom-site position specified as a fraction of attribute length_a in category cell. The standard uncertainty (estimated standard deviation) of attribute fract_x in category atom_site. The y coordinate of the atom-site position specified as a fraction of attribute length_b in category cell. The standard uncertainty (estimated standard deviation) of attribute fract_y in category atom_site. The z coordinate of the atom-site position specified as a fraction of attribute length_c in category cell. The standard uncertainty (estimated standard deviation) of attribute fract_z in category atom_site. The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. A place holder to indicate alternate conformation. The alternate conformation can be an entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. A component of the identifier for this atom site. For further details, see the definition of the STRUCT_ASYM category. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. A component of the identifier for this atom site. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for this atom site. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. The fraction of the atom type present at this site. The sum of the occupancies of all the atom types at this site may not exceed 1.0 unless it is a dummy site. The standard uncertainty (estimated standard deviation) of attribute occupancy in category atom_site. PDB atom name. PDB insertion code. PDB model number. PDB residue name. PDB residue number. PDB strand id. The optional value of attribute pdbx_atom_ambiguity in category atom_site atoms that differ only by stereochemistry but are not stereospecifically assigned by the experiment. HDx% HDy% H5x H5y The ATOM group code used by the NDB. Author's alternate location identifier. Author's strand id. Author's atom name. Author's residue name. Author's sequence identifier. The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 The ATOM group code used by the NDB. Sequential residue number used by NDB. The NCS domain to which the atom position is assigned. The NCS group is defined in category struct_ncs_dom. This item is a reference to attribute id in category struct_ncs_dom. Will identify with a 'Y' that this strand got generated. The value of attribute pdbx_struct_group_id in category atom_site identifies the group or groups assigned to this atom. This is a reference to the identifier for group definition in category PDBX_STRUCT_GROUP_LIST. Multiple groups identifiers are encoded as a comma separated list. atom assigned to individual group C1 C1 atom assigned to multiple groups C1, C2 and C3 C1,C2,C3 The TLS group to which the atom position is assigned. The TLS group is defined in category pdbx_refine_tls. This item is a reference to attribute id in category pdbx_refine_tls. A concatenated series of single-letter codes which indicate the refinement restraints or constraints applied to this site. This item should not be used. It has been replaced by attribute refinement_flags_posn in category atom_site, *_adp and *_occupancy. It is retained in this dictionary only to provide compatibility with old CIFs. A code which indicates the refinement restraints or constraints applied to the atomic displacement parameters of this site. A code which indicates that refinement restraints or constraints were applied to the occupancy of this site. A code which indicates the refinement restraints or constraints applied to the positional coordinates of this site. A description of restraints applied to specific parameters at this site during refinement. See also attribute refinement_flags in category atom_site and attribute ls_number_restraints in category refine. restrained to planar ring The multiplicity of a site due to the space-group symmetry as is given in International Tables for Crystallography Vol. A (2002). A standard code used to describe the type of atomic displacement parameters used for the site. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. The value of attribute id in category atom_site must uniquely identify a record in the ATOM_SITE list. Note that this item need not be a number; it can be any unique identifier. This data item was introduced to provide compatibility between small-molecule and macromolecular CIFs. In a small-molecule CIF, _atom_site_label is the identifier for the atom. In a macromolecular CIF, the atom identifier is the aggregate of _atom_site.label_alt_id, _atom_site.label_asym_id, _atom_site.label_atom_id, _atom_site.label_comp_id and attribute label_seq_id in category atom_site. For the two types of files to be compatible, a formal identifier for the category had to be introduced that was independent of the different modes of identifying the atoms. For compatibility with older CIFs, _atom_site_label is aliased to attribute id. in category atom_site In general, this aggregate identifier does not uniquely identify an atom site as for non-polymers attribute label_seq_id in category atom_site is '.'. 5 C12 Ca3g28 Fe3+17 H*251 boron2a C_a_phe_83_a_0 Zn_Zn_301_A_0 Data items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used. Example 1 - based on NDB structure BDL005 of Holbrook, Dickerson & Kim [Acta Cryst. (1985), B41, 255-262]. <PDBx:atom_site_anisotropCategory> <PDBx:atom_site_anisotrop id="1"> <PDBx:U11>8642</PDBx:U11> <PDBx:U12>4866</PDBx:U12> <PDBx:U13>7299</PDBx:U13> <PDBx:U22>-342</PDBx:U22> <PDBx:U23>-258</PDBx:U23> <PDBx:U33>-1427</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="2"> <PDBx:U11>5174</PDBx:U11> <PDBx:U12>4871</PDBx:U12> <PDBx:U13>6243</PDBx:U13> <PDBx:U22>-1885</PDBx:U22> <PDBx:U23>-2051</PDBx:U23> <PDBx:U33>-1377</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="3"> <PDBx:U11>6202</PDBx:U11> <PDBx:U12>5020</PDBx:U12> <PDBx:U13>4395</PDBx:U13> <PDBx:U22>-1130</PDBx:U22> <PDBx:U23>-556</PDBx:U23> <PDBx:U33>-632</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="4"> <PDBx:U11>4224</PDBx:U11> <PDBx:U12>4700</PDBx:U12> <PDBx:U13>5046</PDBx:U13> <PDBx:U22>1105</PDBx:U22> <PDBx:U23>-161</PDBx:U23> <PDBx:U33>345</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="5"> <PDBx:U11>8684</PDBx:U11> <PDBx:U12>4688</PDBx:U12> <PDBx:U13>4171</PDBx:U13> <PDBx:U22>-1850</PDBx:U22> <PDBx:U23>-433</PDBx:U23> <PDBx:U33>-292</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="6"> <PDBx:U11>11226</PDBx:U11> <PDBx:U12>5255</PDBx:U12> <PDBx:U13>3532</PDBx:U13> <PDBx:U22>-341</PDBx:U22> <PDBx:U23>2685</PDBx:U23> <PDBx:U33>1328</PDBx:U33> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="7"> <PDBx:U11>10214</PDBx:U11> <PDBx:U12>2428</PDBx:U12> <PDBx:U13>5614</PDBx:U13> <PDBx:U22>-2610</PDBx:U22> <PDBx:U23>-1940</PDBx:U23> <PDBx:U33>902</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="8"> <PDBx:U11>4590</PDBx:U11> <PDBx:U12>3488</PDBx:U12> <PDBx:U13>5827</PDBx:U13> <PDBx:U22>751</PDBx:U22> <PDBx:U23>-770</PDBx:U23> <PDBx:U33>986</PDBx:U33> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:atom_site_anisotrop> <PDBx:atom_site_anisotrop id="9"> <PDBx:U11>5014</PDBx:U11> <PDBx:U12>4434</PDBx:U12> <PDBx:U13>3447</PDBx:U13> <PDBx:U22>-17</PDBx:U22> <PDBx:U23>-1593</PDBx:U23> <PDBx:U33>539</PDBx:U33> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:atom_site_anisotrop> </PDBx:atom_site_anisotropCategory> The [1][1] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute B[1][1] in category atom_site_anisotrop. The [1][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute B[1][2] in category atom_site_anisotrop. The [1][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute B[1][3] in category atom_site_anisotrop. The [2][2] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute B[2][2] in category atom_site_anisotrop. The [2][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute B[2][3] in category atom_site_anisotrop. The [3][3] element of the anisotropic atomic displacement matrix B, which appears in the structure-factor term as: T = exp{-1/4 sum~i~[sum~j~(B^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The IUCr Commission on Nomenclature recommends against the use of B for reporting atomic displacement parameters. U, being directly proportional to B, is preferred. The standard uncertainty (estimated standard deviation) of attribute B[3][3] in category atom_site_anisotrop. The [1][1] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute U[1][1] in category atom_site_anisotrop. The [1][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute U[1][2] in category atom_site_anisotrop. The [1][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute U[1][3] in category atom_site_anisotrop. The [2][2] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute U[2][2] in category atom_site_anisotrop. The [2][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute U[2][3] in category atom_site_anisotrop. The [3][3] element of the standard anisotropic atomic displacement matrix U, which appears in the structure-factor term as: T = exp{-2 pi^2^ sum~i~[sum~j~(U^ij^ h~i~ h~j~ a*~i~ a*~j~)]} h = the Miller indices a* = the reciprocal space cell lengths These matrix elements may appear with atomic coordinates in the ATOM_SITE category, or they may appear in the separate ATOM_SITE_ANISOTROP category, but they may not appear in both places. Similarly, anisotropic displacements may appear as either B's or U's, but not as both. The unique elements of the real symmetric matrix are entered by row. The standard uncertainty (estimated standard deviation) of attribute U[3][3] in category atom_site_anisotrop. PDB atom name. Pointer to attribute pdbx_PDB_ins_code in category atom_site Pointer to attribute pdbx_PDB_model_num in category atom_site PDB residue name. PDB residue number. PDB strand id. Pointer to attribute pdbx_auth_alt_id in category atom_site. Pointer to attribute auth_asym_id in category atom_site Pointer to attribute auth_atom_id in category atom_site Author's atom name. Pointer to attribute auth_comp_id in category atom_site Pointer to attribute auth_seq_id in category atom_site Pointer to attribute label_alt_id in category atom_site. Pointer to attribute label_asym_id in category atom_site Pointer to attribute label_atom_id in category atom_site Pointer to attribute label_comp_id in category atom_site NDB INSERTION CODE Pointer to attribute label_seq_id in category atom_site Will identify with a 'Y' that this strand got generated. Ratio of the maximum to minimum principal axes of displacement (thermal) ellipsoids. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sitesCategory> <PDBx:atom_sites entry_id="5HVP"> <PDBx:Cartn_transf_matrix11>58.39</PDBx:Cartn_transf_matrix11> <PDBx:Cartn_transf_matrix12>0.00</PDBx:Cartn_transf_matrix12> <PDBx:Cartn_transf_matrix13>0.00</PDBx:Cartn_transf_matrix13> <PDBx:Cartn_transf_matrix21>0.00</PDBx:Cartn_transf_matrix21> <PDBx:Cartn_transf_matrix22>86.70</PDBx:Cartn_transf_matrix22> <PDBx:Cartn_transf_matrix23>0.00</PDBx:Cartn_transf_matrix23> <PDBx:Cartn_transf_matrix31>0.00</PDBx:Cartn_transf_matrix31> <PDBx:Cartn_transf_matrix32>0.00</PDBx:Cartn_transf_matrix32> <PDBx:Cartn_transf_matrix33>46.27</PDBx:Cartn_transf_matrix33> <PDBx:Cartn_transf_vector1>0.00</PDBx:Cartn_transf_vector1> <PDBx:Cartn_transf_vector2>0.00</PDBx:Cartn_transf_vector2> <PDBx:Cartn_transf_vector3>0.00</PDBx:Cartn_transf_vector3> <PDBx:Cartn_transform_axes>c along z, astar along x, b along y</PDBx:Cartn_transform_axes> </PDBx:atom_sites> </PDBx:atom_sitesCategory> The [1][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [1][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [1][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [2][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [2][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [2][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [3][1] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [3][2] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [3][3] element of the 3x3 matrix used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute Cartn_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [1] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [2] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| The [3] element of the three-element vector used to transform fractional coordinates in the ATOM_SITE category to Cartesian coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The rotation matrix is defined in attribute Cartn_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~Cartesian~ = |21 22 23| |y|~fractional~ + |2| |z'| |31 32 33| |z| |3| A description of the relative alignment of the crystal cell axes to the Cartesian orthogonal axes as applied in the transformation matrix attribute Cartn_transf_matrix[][] in category atom_sites. a parallel to x; b in the plane of y and z The [1][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [1][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [1][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [2][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [2][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [2][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [3][1] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [3][2] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [3][3] element of the 3x3 matrix used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x1 translation is defined in attribute fract_transf_vector[]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [1] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [2] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| The [3] element of the three-element vector used to transform Cartesian coordinates in the ATOM_SITE category to fractional coordinates in the same category. The axial alignments of this transformation are described in attribute Cartn_transform_axes. in category atom_sites The 3x3 rotation is defined in attribute fract_transf_matrix[][]. in category atom_sites |x'| |11 12 13| |x| |1| |y'|~fractional~ = |21 22 23| |y|~Cartesian~ + |2| |z'| |31 32 33| |z| |3| This code identifies the method used to locate the hydrogen atoms. *** This data item would not in general be used in a macromolecular data block. *** This code identifies the method used to locate the initial atom sites. *** This data item would not in general be used in a macromolecular data block. *** This code identifies the method used to locate the non-hydrogen-atom sites not found by attribute solution_primary. in category atom_sites *** This data item would not in general be used in a macromolecular data block. *** Additional information about the atomic coordinates not coded elsewhere in the CIF. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_altCategory> <PDBx:atom_sites_alt id="1"> <PDBx:details> Atom sites with the alternative ID set to 1 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 2. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 1 correlate with the conformation of the inhibitor marked with alternative ID 1. They have been given an occupancy of 0.58 to match the occupancy assigned to the inhibitor.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="2"> <PDBx:details> Atom sites with the alternative ID set to 2 have been modeled in alternative conformations with respect to atom sites marked with alternative ID 1. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 2 correlate with the conformation of the inhibitor marked with alternative ID 2. They have been given an occupancy of 0.42 to match the occupancy assigned to the inhibitor.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="3"> <PDBx:details> Atom sites with the alternative ID set to 3 have been modeled in alternative conformations with respect to atoms marked with alternative ID 4. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 3 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50.</PDBx:details> </PDBx:atom_sites_alt> <PDBx:atom_sites_alt id="4"> <PDBx:details> Atom sites with the alternative ID set to 4 have been modeled in alternative conformations with respect to atoms marked with alternative ID 3. The conformations of amino-acid side chains and solvent atoms with alternative ID set to 4 do not correlate with the conformation of the inhibitor. These atom sites have arbitrarily been given an occupancy of 0.50.</PDBx:details> </PDBx:atom_sites_alt> </PDBx:atom_sites_altCategory> A description of special aspects of the modelling of atoms in alternative conformations. The value of attribute id in category atom_sites_alt must uniquely identify a record in the ATOM_SITES_ALT list. Note that this item need not be a number; it can be any unique identifier. orientation 1 molecule abc Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_alt_ensCategory> <PDBx:atom_sites_alt_ens id="Ensemble 1-A"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 1-B"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the more populated conformation of the inhibitor (ID=1) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 2-A"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=3) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> <PDBx:atom_sites_alt_ens id="Ensemble 2-B"> <PDBx:details> The inhibitor binds to the enzyme in two, roughly twofold symmetric alternative conformations. This conformational ensemble includes the less populated conformation of the inhibitor (ID=2) and the amino-acid side chains and solvent structure that correlate with this inhibitor conformation. Also included are one set (ID=4) of side chains with alternative conformations when the conformations are not correlated with the inhibitor conformation.</PDBx:details> </PDBx:atom_sites_alt_ens> </PDBx:atom_sites_alt_ensCategory> A description of special aspects of the ensemble structure generated from atoms with various alternative IDs. The value of attribute id in category atom_sites_alt_ens must uniquely identify a record in the ATOM_SITES_ALT_ENS list. Note that this item need not be a number; it can be any unique identifier. Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_alt_genCategory> <PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 1-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="1" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 1-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="3" ens_id="Ensemble 2-A"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="2" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen> <PDBx:atom_sites_alt_gen alt_id="4" ens_id="Ensemble 2-B"></PDBx:atom_sites_alt_gen> </PDBx:atom_sites_alt_genCategory> This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. This data item is a pointer to attribute id in category atom_sites_alt_ens in the ATOM_SITES_ALT_ENS category. Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_sites_footnoteCategory> <PDBx:atom_sites_footnote id="1"> <PDBx:text> The inhibitor binds to the enzyme in two alternative orientations. The two orientations have been assigned alternative IDs *1* and *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="2"> <PDBx:text> Side chains of these residues adopt alternative orientations that correlate with the alternative orientations of the inhibitor. Side chains with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Side chains with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="3"> <PDBx:text> The positions of these water molecules correlate with the alternative orientations of the inhibitor. Water molecules with alternative ID *1* and occupancy 0.58 correlate with inhibitor orientation *1*. Water molecules with alternative ID *2* and occupancy 0.42 correlate with inhibitor orientation *2*.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="4"> <PDBx:text> Side chains of these residues adopt alternative orientations that do not correlate with the alternative orientation of the inhibitor.</PDBx:text> </PDBx:atom_sites_footnote> <PDBx:atom_sites_footnote id="5"> <PDBx:text> The positions of these water molecules correlate with alternative orientations of amino-acid side chains that do not correlate with alternative orientations of the inhibitor.</PDBx:text> </PDBx:atom_sites_footnote> </PDBx:atom_sites_footnoteCategory> The text of the footnote. Footnotes are used to describe an atom site or a group of atom sites in the ATOM_SITE list. For example, footnotes may be used to indicate atoms for which the electron density is very weak, or atoms for which static disorder has been modelled. A code that identifies the footnote. a b 1 2 Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:atom_typeCategory> <PDBx:atom_type symbol="C"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>2.31000</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>20.8439</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>1.02000</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>10.2075</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.58860</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.568700</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>0.865000</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>51.6512</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.21560</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="N"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>12.2126</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>0.005700</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>3.13220</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>9.89330</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>2.01250</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>28.9975</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>1.16630</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>0.582600</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>-11.529</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="O"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>3.04850</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>13.2771</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>2.28680</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>5.70110</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.54630</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.323900</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>0.867000</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>32.9089</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.250800</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="S"> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>6.90530</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>1.46790</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>5.20340</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>22.2151</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>1.43790</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>0.253600</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>1.58630</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>56.1720</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>0.866900</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> <PDBx:atom_type symbol="CL"> <PDBx:oxidation_number>-1</PDBx:oxidation_number> <PDBx:scat_Cromer_Mann_a1>18.2915</PDBx:scat_Cromer_Mann_a1> <PDBx:scat_Cromer_Mann_a2>0.006600</PDBx:scat_Cromer_Mann_a2> <PDBx:scat_Cromer_Mann_a3>7.20840</PDBx:scat_Cromer_Mann_a3> <PDBx:scat_Cromer_Mann_a4>1.17170</PDBx:scat_Cromer_Mann_a4> <PDBx:scat_Cromer_Mann_b1>6.53370</PDBx:scat_Cromer_Mann_b1> <PDBx:scat_Cromer_Mann_b2>19.5424</PDBx:scat_Cromer_Mann_b2> <PDBx:scat_Cromer_Mann_b3>2.33860</PDBx:scat_Cromer_Mann_b3> <PDBx:scat_Cromer_Mann_b4>60.4486</PDBx:scat_Cromer_Mann_b4> <PDBx:scat_Cromer_Mann_c>-16.378</PDBx:scat_Cromer_Mann_c> </PDBx:atom_type> </PDBx:atom_typeCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:atom_typeCategory> <PDBx:atom_type symbol="C"> <PDBx:number_in_cell>72</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.009</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.017</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="H"> <PDBx:number_in_cell>100</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>0</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>0</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="O"> <PDBx:number_in_cell>12</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.032</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.047</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> <PDBx:atom_type symbol="N"> <PDBx:number_in_cell>4</PDBx:number_in_cell> <PDBx:oxidation_number>0</PDBx:oxidation_number> <PDBx:scat_dispersion_imag>.018</PDBx:scat_dispersion_imag> <PDBx:scat_dispersion_real>.029</PDBx:scat_dispersion_real> <PDBx:scat_source>International_Tables_Vol_IV_Table_2.2B</PDBx:scat_source> </PDBx:atom_type> </PDBx:atom_typeCategory> Mass percentage of this atom type derived from chemical analysis. A description of the atom(s) designated by this atom type. In most cases, this is the element name and oxidation state of a single atom species. For disordered or nonstoichiometric structures it will describe a combination of atom species. deuterium 0.34Fe+0.66Ni Total number of atoms of this atom type in the unit cell. Formal oxidation state of this atom type in the structure. Number of electrons in atom used in scattering factor Scattering-factor coefficient a5, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. Scattering-factor coefficient a6, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. Scattering-factor coefficient b5, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. Scattering-factor coefficient b6, used to calculate electron elastic atomic scattering factors for the defined atom type. Electron Elastic Scattering Factors Ref: International Tables for X-ray Crystallography (2006). Vol. C, Table 4.3.2.2, pp. 282-283. Cromer_Mann equation Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. Atomic number of atom in scattering amplitude. The effective intramolecular bonding radius in angstroms of this atom type. The effective intermolecular bonding radius in angstroms of this atom type. The Cromer-Mann scattering-factor coefficient a1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient a2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient a3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient a4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient b1 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient b2 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient b3 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient b4 used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The Cromer-Mann scattering-factor coefficient c used to calculate the scattering factors for this atom type. Ref: International Tables for X-ray Crystallography (1974). Vol. IV, Table 2.2B or: International Tables for Crystallography (2004). Vol. C, Tables 6.1.1.4 and 6.1.1.5. The imaginary component of the anomalous-dispersion scattering factor, f'', in electrons for this atom type and the radiation identified by attribute id in category diffrn_radiation_wavelength. The real component of the anomalous-dispersion scattering factor, f', in electrons for this atom type and the radiation identified by attribute id in category diffrn_radiation_wavelength. Reference to the source of the real and imaginary dispersion corrections for scattering factors used for this atom type. International Tables Vol. IV Table 2.3.1 The bound coherent scattering length in femtometres for the atom type at the isotopic composition used for the diffraction experiment. Reference to the source of the scattering factors or scattering lengths used for this atom type. International Tables Vol. IV Table 2.4.6B A table of scattering factors as a function of sin theta over lambda. This table should be well commented to indicate the items present. Regularly formatted lists are strongly recommended. The code used to identify the atom species (singular or plural) representing this atom type. Normally this code is the element symbol. The code may be composed of any character except an underscore with the additional proviso that digits designate an oxidation state and must be followed by a + or - character. C Cu2+ H(SDS) dummy FeNi Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items in the JOURNAL category that record different stages in the publication of the material in the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:auditCategory> <PDBx:audit revision_id="1"> <PDBx:creation_date>1992-12-08</PDBx:creation_date> <PDBx:creation_method> Created by hand from PDB entry 5HVP, from the J. Biol. Chem. paper describing this structure and from laboratory records</PDBx:creation_method> <PDBx:update_record> 1992-12-09 adjusted to reflect comments from B. McKeever 1992-12-10 adjusted to reflect comments from H. Berman 1992-12-12 adjusted to reflect comments from K. Watenpaugh</PDBx:update_record> </PDBx:audit> </PDBx:auditCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:auditCategory> <PDBx:audit revision_id="2"> <PDBx:creation_date>1991-03-20</PDBx:creation_date> <PDBx:creation_method>from_xtal_archive_file_using_CIFIO</PDBx:creation_method> <PDBx:update_record> 1991-04-09 text and data added by Tony Willis. 1991-04-15 rec&apos;d by co-editor as manuscript HL0007. 1991-04-17 adjustments based on first referee report. 1991-04-18 adjustments based on second referee report.</PDBx:update_record> </PDBx:audit> </PDBx:auditCategory> A date that the data block was created. The date format is yyyy-mm-dd. 1990-07-12 A description of how data were entered into the data block. spawned by the program QBEE A record of any changes to the data block. The update format is a date (yyyy-mm-dd) followed by a description of the changes. The latest update entry is added to the bottom of this record. 1990-07-15 Updated by the Co-editor The value of attribute revision_id in category audit must uniquely identify a record in the AUDIT list. rev1 Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:audit_authorCategory> <PDBx:audit_author pdbx_ordinal="1"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Fitzgerald, Paula M.D.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="2"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>McKeever, Brian M.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="3"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Van Middlesworth, J.F.</PDBx:name> </PDBx:audit_author> <PDBx:audit_author pdbx_ordinal="4"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Springer, James P.</PDBx:name> </PDBx:audit_author> </PDBx:audit_authorCategory> The address of an author of this data block. If there are multiple authors, attribute address in category audit_author is looped with attribute name in category audit_author. Department Institute Street City and postcode COUNTRY The Open Researcher and Contributor ID (ORCID). 0000-0002-6681-547X The name of an author of this data block. If there are multiple authors, _audit_author.name is looped with _audit_author.address. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A This data item defines the order of the author's name in the list of audit authors. 1 2 3 Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. Example 1 - any file conforming to the current CIF core dictionary. <PDBx:audit_conformCategory> <PDBx:audit_conform dict_name="cif_core.dic" dict_version="2.3.1"> <PDBx:dict_location>ftp://ftp.iucr.org/pub/cif_core.2.3.1.dic</PDBx:dict_location> </PDBx:audit_conform> </PDBx:audit_conformCategory> A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. The string identifying the highest-level dictionary defining data names used in this file. The version number of the dictionary to which the current data block conforms. Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:audit_contact_authorCategory> <PDBx:audit_contact_author name="Fitzgerald, Paula M.D."> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories PO Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:email>paula_fitzgerald@merck.com</PDBx:email> <PDBx:fax>1(908)5946645</PDBx:fax> <PDBx:phone>1(908)5945510</PDBx:phone> </PDBx:audit_contact_author> </PDBx:audit_contact_authorCategory> The mailing address of the author of the data block to whom correspondence should be addressed. Department Institute Street City and postcode COUNTRY The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. name@host.domain.country bm@iucr.org The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. 12(34)9477334 12()349477334 The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. 12(34)9477330 12()349477330 12(34)9477330x5543 The name of the author of the data block to whom correspondence should be addressed. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF. Example 1 - multiple structure paper, as illustrated in A Guide to CIF for Authors (1995). IUCr: Chester. <PDBx:audit_linkCategory> <PDBx:audit_link block_code="morA_pub" block_description="discursive text of paper with two structures"></PDBx:audit_link> <PDBx:audit_link block_code="morA_(1)" block_description="structure 1 of 2"></PDBx:audit_link> <PDBx:audit_link block_code="morA_(2)" block_description="structure 2 of 2"></PDBx:audit_link> </PDBx:audit_linkCategory> Example 2 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <PDBx:audit_linkCategory> <PDBx:audit_link block_code="KSE_PUB" block_description="publication details"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_COM" block_description="experimental data common to ref./mod. structures"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_REF" block_description="reference structure"></PDBx:audit_link> <PDBx:audit_link block_code="KSE_MOD" block_description="modulated structure"></PDBx:audit_link> </PDBx:audit_linkCategory> The value of attribute code in category audit_block associated with a data block in the current file related to the current data block. The special value '.' may be used to refer to the current data block for completeness. A textual description of the relationship of the referenced data block to the current one. Data items in the CELL category record details about the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:cellCategory> <PDBx:cell entry_id="5HVP"> <PDBx:angle_alpha>90.00</PDBx:angle_alpha> <PDBx:angle_beta>90.00</PDBx:angle_beta> <PDBx:angle_gamma>90.00</PDBx:angle_gamma> <PDBx:details> The cell parameters were refined every twenty frames during data integration. The cell lengths given are the mean of 55 such refinements; the esds given are the root mean square deviations of these 55 observations from that mean.</PDBx:details> <PDBx:length_a>58.39</PDBx:length_a> <PDBx:length_a_esd>0.05</PDBx:length_a_esd> <PDBx:length_b>86.70</PDBx:length_b> <PDBx:length_b_esd>0.12</PDBx:length_b_esd> <PDBx:length_c>46.27</PDBx:length_c> <PDBx:length_c_esd>0.06</PDBx:length_c_esd> <PDBx:volume>234237</PDBx:volume> </PDBx:cell> </PDBx:cellCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:cellCategory> <PDBx:cell entry_id="1TOZ"> <PDBx:angle_alpha>90.0</PDBx:angle_alpha> <PDBx:angle_beta>90.0</PDBx:angle_beta> <PDBx:angle_gamma>90.0</PDBx:angle_gamma> <PDBx:length_a>5.959</PDBx:length_a> <PDBx:length_a_esd>0.001</PDBx:length_a_esd> <PDBx:length_b>14.956</PDBx:length_b> <PDBx:length_b_esd>0.001</PDBx:length_b_esd> <PDBx:length_c>19.737</PDBx:length_c> <PDBx:length_c_esd>0.003</PDBx:length_c_esd> <PDBx:volume>1759.0</PDBx:volume> <PDBx:volume_esd>0.3</PDBx:volume_esd> </PDBx:cell> </PDBx:cellCategory> The number of the polymeric chains in a unit cell. In the case of heteropolymers, Z is the number of occurrences of the most populous chain. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose. Unit-cell angle alpha of the reported structure in degrees. The standard uncertainty (estimated standard deviation) of attribute angle_alpha in category cell. Unit-cell angle beta of the reported structure in degrees. The standard uncertainty (estimated standard deviation) of attribute angle_beta in category cell. Unit-cell angle gamma of the reported structure in degrees. The standard uncertainty (estimated standard deviation) of attribute angle_gamma in category cell. A description of special aspects of the cell choice, noting possible alternative settings. pseudo-orthorhombic standard setting from 45 deg rotation around c The number of the formula units in the unit cell as specified by _chemical_formula.structural, _chemical_formula.moiety or attribute sum in category chemical_formula. Unit-cell length a corresponding to the structure reported in angstroms. The standard uncertainty (estimated standard deviation) of attribute length_a in category cell. Unit-cell length b corresponding to the structure reported in angstroms. The standard uncertainty (estimated standard deviation) of attribute length_b in category cell. Unit-cell length c corresponding to the structure reported in angstroms. The standard uncertainty (estimated standard deviation) of attribute length_c in category cell. To further identify unique axis if necessary. E.g., P 21 with an unique C axis will have 'C' in this field. The angle (recip-alpha) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. The estimated standard deviation of attribute reciprocal_angle_alpha in category cell. The angle (recip-beta) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. The estimated standard deviation of attribute reciprocal_angle_beta in category cell. The angle (recip-gamma) defining the reciprocal cell in degrees. (recip-alpha), (recip-alpha) and (recip-alpha) related to the angles in the real cell by: cos(recip-alpha) = [cos(beta)*cos(gamma) - cos(alpha)]/[sin(beta)*sin(gamma)] cos(recip-beta) = [cos(gamma)*cos(alpha) - cos(beta)]/[sin(gamma)*sin(alpha)] cos(recip-gamma) = [cos(alpha)*cos(beta) - cos(gamma)]/[sin(alpha)*sin(beta)] Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. The estimated standard deviation of attribute reciprocal_angle_gamma in category cell. The reciprocal cell length (recip-a) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. The estimated standard deviation of attribute reciprocal_length_a in category cell. The reciprocal cell length (recip-b) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. The estimated standard deviation of attribute reciprocal_length_b in category cell. The reciprocal cell length (recip-c) in inverse Angstroms. (recip-a), (recip-b) and (recip-c) are related to the real cell by the following equation: recip-a = b*c*sin(alpha)/V recip-b = c*a*sin(beta)/V recip-c = a*b*sin(gamma)/V where V is the cell volume. Ref: Buerger, M. J. (1942). X-ray Crystallography, p. 360. New York: John Wiley & Sons Inc. The estimated standard deviation of attribute reciprocal_length_c in category cell. Cell volume V in angstroms cubed. V = a b c (1 - cos^2^~alpha~ - cos^2^~beta~ - cos^2^~gamma~ + 2 cos~alpha~ cos~beta~ cos~gamma~)^1/2^ a = attribute length_a in category cell b = attribute length_b in category cell c = attribute length_c in category cell alpha = attribute angle_alpha in category cell beta = attribute angle_beta in category cell gamma = attribute angle_gamma in category cell The standard uncertainty (estimated standard deviation) of attribute volume in category cell. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:cell_measurementCategory> <PDBx:cell_measurement entry_id="5HVP"> <PDBx:temp>293</PDBx:temp> <PDBx:temp_esd>3</PDBx:temp_esd> <PDBx:theta_max>31</PDBx:theta_max> <PDBx:theta_min>11</PDBx:theta_min> <PDBx:wavelength>1.54</PDBx:wavelength> </PDBx:cell_measurement> </PDBx:cell_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:cell_measurementCategory> <PDBx:cell_measurement entry_id="1TOZ"> <PDBx:reflns_used>25</PDBx:reflns_used> <PDBx:temp>293</PDBx:temp> <PDBx:theta_max>31</PDBx:theta_max> <PDBx:theta_min>25</PDBx:theta_min> </PDBx:cell_measurement> </PDBx:cell_measurementCategory> The pressure in kilopascals at which the unit-cell parameters were measured (not the pressure at which the sample was synthesized). The standard uncertainty (estimated standard deviation) of attribute pressure in category cell_measurement. Description of the radiation used to measure the unit-cell data. See also attribute wavelength in category cell_measurement. neutron Cu K\a synchrotron The total number of reflections used to determine the unit cell. These reflections may be specified as CELL_MEASUREMENT_REFLN data items. The temperature in kelvins at which the unit-cell parameters were measured (not the temperature of synthesis). The standard uncertainty (estimated standard deviation) of attribute temp in category cell_measurement. The maximum theta angle of reflections used to measure the unit cell in degrees. The minimum theta angle of reflections used to measure the unit cell in degrees. The wavelength in angstroms of the radiation used to measure the unit cell. If this is not specified, the wavelength is assumed to be that specified in the category DIFFRN_RADIATION_WAVELENGTH. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data. Example 1 - extracted from the CAD-4 listing of Rb~2~S~2~O~6~ at room temperature (unpublished). <PDBx:cell_measurement_reflnCategory> <PDBx:cell_measurement_refln index_h="-2" index_k="4" index_l="1"> <PDBx:theta>8.67</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="0" index_k="3" index_l="2"> <PDBx:theta>9.45</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="3" index_k="0" index_l="2"> <PDBx:theta>9.46</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-3" index_k="4" index_l="1"> <PDBx:theta>8.93</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-2" index_k="1" index_l="-2"> <PDBx:theta>7.53</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="10" index_k="0" index_l="0"> <PDBx:theta>23.77</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="0" index_k="10" index_l="0"> <PDBx:theta>23.78</PDBx:theta> </PDBx:cell_measurement_refln> <PDBx:cell_measurement_refln index_h="-5" index_k="4" index_l="1"> <PDBx:theta>11.14</PDBx:theta> </PDBx:cell_measurement_refln> </PDBx:cell_measurement_reflnCategory> Theta angle for a reflection used for measurement of the unit cell in degrees. Miller index h of a reflection used for measurement of the unit cell. Miller index k of a reflection used for measurement of the unit cell. Miller index l of a reflection used for measurement of the unit cell. Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_compCategory> <PDBx:chem_comp id="phe"> <PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source> <PDBx:name>phenylalanine</PDBx:name> </PDBx:chem_comp> <PDBx:chem_comp id="val"> <PDBx:model_source>1987 Protin/Prolsq Ideals file</PDBx:model_source> <PDBx:name>alanine</PDBx:name> </PDBx:chem_comp> </PDBx:chem_compCategory> The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S Formula mass in daltons of the chemical component. A description of special aspects of the generation of the coordinates for the model of the component. geometry idealized but not minimized A pointer to an external reference file from which the atomic description of the component is taken. The source of the coordinates for the model of the component. CSD entry ABCDEF built using Quanta/Charmm A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer. iodinated base phosphorylated amino acid brominated base modified amino acid glycosylated amino acid A description of special details of a nonstandard monomer. 'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and attribute mon_nstd_details in category chem_comp data items. The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer. tyrosine cytosine The identifier for the parent component of the nonstandard component. May be be a comma separated list if this component is derived from multiple components. Items in this indirectly point to attribute id in category chem_comp in the CHEM_COMP category. The full name of the component. alanine valine adenine cytosine The total number of atoms in the component. The number of non-hydrogen atoms in the component. For standard polymer components, the one-letter code for the component. For non-standard polymer components, the one-letter code for parent component if this exists; otherwise, the one-letter code should be given as 'X'. Components that derived from multiple parents components are described by a sequence of one-letter-codes. alanine or adenine A ambiguous asparagine/aspartic acid B arginine R asparagine N aspartic acid D cysteine or cystine or cytosine C glutamine Q glutamic acid E ambiguous glutamine/glutamic acid Z glycine or guanine G histidine H isoleucine I leucine L lysine K methionine M phenylalanine F proline P serine S threonine or thymine T tryptophan W tyrosine Y valine V uracil U water O other X A preliminary classification used by PDB to indicate that the chemistry of this component while described as clearly as possible is still ambiguous. Software tools may not be able to process this component definition. Chemical Abstract Service identifier. Internal classifier used to organize ligand dictionary (broad chemical class). HETEROCYCLIC AROMATIC COMPOUNDS Internal classifier used to organize ligand dictionary (notable chemical features). COMPOUNDS WITH THIAZOLIDINE A type classification of this chemical component. A serial number used by PDB in the FORMUL record. 3 The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams. This data item identifies the source of the ideal coordinates in the component definition. This data item identifies if ideal coordinates are missing in this definition. Date component was added to database. This data item identifies the PDB database code from which the heavy atom model coordinates were obtained. This data item provides additional details about the model coordinates in the component definition. This data item identifies if model coordinates are missing in this definition. For nonstandard components a text description of modification of the parent component. ATP Date component was last modified. NSC identifier for component. The number of subcomponents represented in this component. This data item identifies the deposition site that processed this chemical component defintion. This data item holds the current release status for the component. Identifies the attribute id in category chem_comp of the component that has replaced this component. q11 tvx Identifies the attribute id's in category chem_comp of the components which have been replaced by this component. Multiple id codes should be separated by commas. q11 tvx,atv Previous chemical name used for this component if a name correction has been made. SMILES code for component. Release status of component The list of subcomponents contained in this component. TSM DPH HIS CHF EMR Synonym list for the component. ATP A preliminary classification used by PDB. Modification flag. For standard polymer components, the common three-letter code for the component. Non-standard polymer components and non-polymer components are also assigned three-letter-codes. For ambiguous polymer components three-letter code should be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'. Ambiguous non-polymer components are assigned the code 'UNL'. alanine ALA arginine ARG asparagine ASN aspartic acid ASP ambiguous asparagine/aspartic acid ASX cysteine CYS glutamine GLN glutamic acid GLU glycine GLY ambiguous glutamine/glutamic acid GLX histidine HIS isoleucine ILE leucine LEU lysine LYS methionine MET phenylalanine PHE proline PRO serine SER threonine THR tryptophan TRP tyrosine TYR valine VAL 1-methyladenosine 1MA 5-methylcytosine 5MC 2(prime)-O-methylcytodine OMC 1-methylguanosine 1MG N(2)-methylguanosine 2MG N(2)-dimethylguanosine M2G 7-methylguanosine 7MG 2(prime)-O-methylguanosine 0MG dihydrouridine H2U ribosylthymidine 5MU pseudouridine PSU acetic acid ACE formic acid FOR water HOH other UNK For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap. The value of attribute id in category chem_comp must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base. ALA VAL DG C Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_angleCategory> <PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" comp_id="PHE"> <PDBx:value_angle>110.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="N" atom_id_2="CA" atom_id_3="CB" comp_id="PHE"> <PDBx:value_angle>110.1</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="CB" comp_id="PHE"> <PDBx:value_angle>110.3</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="C" atom_id_2="CA" atom_id_3="HA" comp_id="PHE"> <PDBx:value_angle>108.3</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" comp_id="PHE"> <PDBx:value_angle>118.4</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="C" atom_id_3="OXT" comp_id="PHE"> <PDBx:value_angle>117.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CA" atom_id_2="CB" atom_id_3="CG" comp_id="PHE"> <PDBx:value_angle>114.0</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="O" atom_id_2="C" atom_id_3="OXT" comp_id="PHE"> <PDBx:value_angle>123.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD1" comp_id="PHE"> <PDBx:value_angle>120.8</PDBx:value_angle> </PDBx:chem_comp_angle> <PDBx:chem_comp_angle atom_id_1="CB" atom_id_2="CG" atom_id_3="CD2" comp_id="PHE"> <PDBx:value_angle>120.5</PDBx:value_angle> </PDBx:chem_comp_angle> </PDBx:chem_comp_angleCategory> The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. The standard uncertainty (estimated standard deviation) of attribute value_angle in category chem_comp_angle. The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by attribute atom_id_1 in category chem_comp_angle and attribute atom_id_3 in category chem_comp_angle. The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle. The ID of the first of the three atoms that define the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The ID of the third of the three atoms that define the angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_atomCategory> <PDBx:chem_comp_atom atom_id="N" comp_id="phe"> <PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CA" comp_id="phe"> <PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="C" comp_id="phe"> <PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="O" comp_id="phe"> <PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CB" comp_id="phe"> <PDBx:model_Cartn_x>0.00662</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-1.03603</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>1.11081</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG" comp_id="phe"> <PDBx:model_Cartn_x>0.03254</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.49711</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>2.50951</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CD1" comp_id="phe"> <PDBx:model_Cartn_x>-1.15813</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.12084</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>3.13467</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CE1" comp_id="phe"> <PDBx:model_Cartn_x>-1.15720</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.38038</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>4.42732</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CZ" comp_id="phe"> <PDBx:model_Cartn_x>0.05385</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.51332</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>5.11032</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CE2" comp_id="phe"> <PDBx:model_Cartn_x>1.26137</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.11613</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>4.50975</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CD2" comp_id="phe"> <PDBx:model_Cartn_x>1.23668</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.38351</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>3.20288</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="N" comp_id="val"> <PDBx:model_Cartn_x>1.20134</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.84658</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CA" comp_id="val"> <PDBx:model_Cartn_x>0.00000</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.00000</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="C" comp_id="val"> <PDBx:model_Cartn_x>-1.25029</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.88107</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.00000</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="O" comp_id="val"> <PDBx:model_Cartn_x>-2.18525</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>0.66029</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>-0.78409</PDBx:model_Cartn_z> <PDBx:substruct_code>main</PDBx:substruct_code> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CB" comp_id="val"> <PDBx:model_Cartn_x>0.05260</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.99339</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>1.17429</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG1" comp_id="val"> <PDBx:model_Cartn_x>-0.13288</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-0.31545</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>2.52668</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> <PDBx:chem_comp_atom atom_id="CG2" comp_id="val"> <PDBx:model_Cartn_x>-0.94265</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>-2.12930</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>0.99811</PDBx:model_Cartn_z> <PDBx:substruct_code>side</PDBx:substruct_code> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chem_comp_atom> </PDBx:chem_comp_atomCategory> An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 The x component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. The standard uncertainty (estimated standard deviation) of attribute model_Cartn_x in category chem_comp_atom. The y component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. The standard uncertainty (estimated standard deviation) of attribute model_Cartn_y in category chem_comp_atom. The z component of the coordinates for this atom in this component specified as orthogonal angstroms. The choice of reference axis frame for the coordinates is arbitrary. The set of coordinates input for the entity here is intended to correspond to the atomic model used to generate restraints for structure refinement, not to atom sites in the ATOM_SITE list. The standard uncertainty (estimated standard deviation) of attribute model_Cartn_z in category chem_comp_atom. The partial charge assigned to this atom. Atom name alignment offset in PDB atom field. An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. An alternative identifier for the atom. This data item would be used in cases where alternative nomenclatures exist for labelling atoms in a group. A flag indicating an aromatic atom. The atom identifier in the subcomponent where a larger component has been divided subcomponents. CB CA CG The component identifier for the subcomponent where a larger component has been divided subcomponents. HIS PRO A reference to entity identifier in data category pdbx_chem_comp_subcomponent_entity_list. A reference to attribute component_id in category pdbx_reference_entity_list A flag indicating a leaving atom. An alternative x component of the coordinates for this atom in this component specified as orthogonal angstroms. An alternative y component of the coordinates for this atom in this component specified as orthogonal angstroms. An alternative z component of the coordinates for this atom in this component specified as orthogonal angstroms. Ordinal index for the component atom list. Is the atom in a polymer or non-polymer subcomponent in the BIRD definition. A reference to attribute ref_entity_id in category pdbx_reference_entity_list Preferred residue numbering in the BIRD definition. The chiral configuration of the atom that is a chiral center. A standard identifier for the atom. This data item is used when IUPAC/IUBMB nomenclature exists for labeling atoms. This data item assigns the atom to a substructure of the component, if appropriate. The code used to identify the atom species representing this atom type. Normally this code is the element symbol. C N O The value of attribute atom_id in category chem_comp_atom must uniquely identify each atom in each monomer in the CHEM_COMP_ATOM list. The atom identifiers need not be unique over all atoms in the data block; they need only be unique for each atom in a component. Note that this item need not be a number; it can be any unique identifier. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_bondCategory> <PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="phe"> <PDBx:value_order>doub</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG" comp_id="phe"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CG" atom_id_2="CD1" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CD1" atom_id_2="CE1" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CE1" atom_id_2="CZ" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CZ" atom_id_2="CE2" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CE2" atom_id_2="CD2" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CD2" atom_id_2="CG" comp_id="phe"> <PDBx:value_order>arom</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="N" atom_id_2="CA" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CA" atom_id_2="C" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="C" atom_id_2="O" comp_id="val"> <PDBx:value_order>doub</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CA" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG1" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> <PDBx:chem_comp_bond atom_id_1="CB" atom_id_2="CG2" comp_id="val"> <PDBx:value_order>sing</PDBx:value_order> </PDBx:chem_comp_bond> </PDBx:chem_comp_bondCategory> A flag indicating an aromatic bond. Ordinal index for the component bond list. Stereochemical configuration across a double bond. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_bond. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. The ID of the first of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The ID of the second of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_chirCategory> <PDBx:chem_comp_chir comp_id="phe" id="phe1"> <PDBx:atom_id>CA</PDBx:atom_id> </PDBx:chem_comp_chir> <PDBx:chem_comp_chir comp_id="val" id="val1"> <PDBx:atom_id>CA</PDBx:atom_id> </PDBx:chem_comp_chir> </PDBx:chem_comp_chirCategory> The chiral configuration of the atom that is a chiral centre. The ID of the atom that is a chiral centre. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The total number of atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir. The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_comp_chir. A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. The chiral volume, V~c~, for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the first atom in the CHEM_COMP_CHIR_ATOM list V2 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the second atom in the CHEM_COMP_CHIR_ATOM list V3 = the vector distance from the atom specified by attribute atom_id in category chem_comp_chir to the third atom in the CHEM_COMP_CHIR_ATOM list * = the vector dot product X = the vector cross product The standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_comp_chir. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The value of attribute id in category chem_comp_chir must uniquely identify a record in the CHEM_COMP_CHIR list. Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_chir_atomCategory> <PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="phe"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="N" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="C" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> <PDBx:chem_comp_chir_atom atom_id="CB" chir_id="1" comp_id="val"></PDBx:chem_comp_chir_atom> </PDBx:chem_comp_chir_atomCategory> The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. The ID of an atom bonded to the chiral atom. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp_chir in the CHEM_COMP_CHIR category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the CHEM_COMP_LINK category give details about the links between chemical components. A description of special aspects of a link between chemical components in the structure. The type of the first of the two components joined by the link. This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP category. The type of the second of the two components joined by the link. This data item is a pointer to attribute type in category chem_comp in the CHEM_COMP category. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_planeCategory> <PDBx:chem_comp_plane comp_id="phe" id="phe1"></PDBx:chem_comp_plane> </PDBx:chem_comp_planeCategory> The total number of atoms in the plane. The number of non-hydrogen atoms in the plane. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The value of attribute id in category chem_comp_plane must uniquely identify a record in the CHEM_COMP_PLANE list. Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_plane_atomCategory> <PDBx:chem_comp_plane_atom atom_id="CB" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CG" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CD1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CE1" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CZ" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CE2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> <PDBx:chem_comp_plane_atom atom_id="CD2" comp_id="phe" plane_id="phe1"></PDBx:chem_comp_plane_atom> </PDBx:chem_comp_plane_atomCategory> This data item is the standard deviation of the out-of-plane distance for this atom. The ID of an atom involved in the plane. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. This data item is a pointer to attribute id in category chem_comp_plane in the CHEM_COMP_PLANE category. Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_torCategory> <PDBx:chem_comp_tor comp_id="phe" id="phe_chi1"> <PDBx:atom_id_1>N</PDBx:atom_id_1> <PDBx:atom_id_2>CA</PDBx:atom_id_2> <PDBx:atom_id_3>CB</PDBx:atom_id_3> <PDBx:atom_id_4>CG</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_chi2"> <PDBx:atom_id_1>CA</PDBx:atom_id_1> <PDBx:atom_id_2>CB</PDBx:atom_id_2> <PDBx:atom_id_3>CG</PDBx:atom_id_3> <PDBx:atom_id_4>CD1</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring1"> <PDBx:atom_id_1>CB</PDBx:atom_id_1> <PDBx:atom_id_2>CG</PDBx:atom_id_2> <PDBx:atom_id_3>CD1</PDBx:atom_id_3> <PDBx:atom_id_4>CE1</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring2"> <PDBx:atom_id_1>CB</PDBx:atom_id_1> <PDBx:atom_id_2>CG</PDBx:atom_id_2> <PDBx:atom_id_3>CD2</PDBx:atom_id_3> <PDBx:atom_id_4>CE2</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring3"> <PDBx:atom_id_1>CG</PDBx:atom_id_1> <PDBx:atom_id_2>CD1</PDBx:atom_id_2> <PDBx:atom_id_3>CE1</PDBx:atom_id_3> <PDBx:atom_id_4>CZ</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring4"> <PDBx:atom_id_1>CD1</PDBx:atom_id_1> <PDBx:atom_id_2>CE1</PDBx:atom_id_2> <PDBx:atom_id_3>CZ</PDBx:atom_id_3> <PDBx:atom_id_4>CE2</PDBx:atom_id_4> </PDBx:chem_comp_tor> <PDBx:chem_comp_tor comp_id="phe" id="phe_ring5"> <PDBx:atom_id_1>CE1</PDBx:atom_id_1> <PDBx:atom_id_2>CZ</PDBx:atom_id_2> <PDBx:atom_id_3>CE2</PDBx:atom_id_3> <PDBx:atom_id_4>CD2</PDBx:atom_id_4> </PDBx:chem_comp_tor> </PDBx:chem_comp_torCategory> The ID of the first of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The ID of the second of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The ID of the third of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. The ID of the fourth of the four atoms that define the torsion angle. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The value of attribute id in category chem_comp_tor must uniquely identify a record in the CHEM_COMP_TOR list. Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:chem_comp_tor_valueCategory> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>-60.0</PDBx:angle> <PDBx:dist>2.88</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.72</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi1"> <PDBx:angle>60.0</PDBx:angle> <PDBx:dist>2.88</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2"> <PDBx:angle>90.0</PDBx:angle> <PDBx:dist>3.34</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_chi2"> <PDBx:angle>-90.0</PDBx:angle> <PDBx:dist>3.34</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring1"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.75</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring2"> <PDBx:angle>180.0</PDBx:angle> <PDBx:dist>3.75</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring3"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring4"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> <PDBx:chem_comp_tor_value comp_id="phe" tor_id="phe_ring5"> <PDBx:angle>0.0</PDBx:angle> <PDBx:dist>2.80</PDBx:dist> </PDBx:chem_comp_tor_value> </PDBx:chem_comp_tor_valueCategory> A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. The standard uncertainty (estimated standard deviation) of attribute angle in category chem_comp_tor_value. A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_tor.atom_id_1 and _chem_comp_tor.atom_id_4 in the referenced record in the CHEM_COMP_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. The standard uncertainty (estimated standard deviation) of attribute dist in category chem_comp_tor_value. This data item is a pointer to attribute comp_id in category chem_comp_atom in the CHEM_COMP_ATOM category. This data item is a pointer to attribute id in category chem_comp_tor in the CHEM_COMP_TOR category. Data items in the CHEM_LINK category give details about the links between chemical components. A description of special aspects of a link between chemical components in the structure. The value of attribute id in category chem_link must uniquely identify each item in the CHEM_LINK list. peptide oligosaccharide 1,4 DNA Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components. Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. <PDBx:chem_link_angleCategory> <PDBx:chem_link_angle atom_id_1="N" atom_id_2="CA" atom_id_3="C" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id> <PDBx:value_angle>111.2</PDBx:value_angle> <PDBx:value_angle_esd>2.8</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="O" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>1</PDBx:atom_3_comp_id> <PDBx:value_angle>120.8</PDBx:value_angle> <PDBx:value_angle_esd>1.7</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="CA" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>116.2</PDBx:value_angle> <PDBx:value_angle_esd>2.0</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="O" atom_id_2="C" atom_id_3="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>123.0</PDBx:value_angle> <PDBx:value_angle_esd>1.6</PDBx:value_angle_esd> </PDBx:chem_link_angle> <PDBx:chem_link_angle atom_id_1="C" atom_id_2="N" atom_id_3="CA" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id> <PDBx:atom_3_comp_id>2</PDBx:atom_3_comp_id> <PDBx:value_angle>121.7</PDBx:value_angle> <PDBx:value_angle_esd>1.8</PDBx:value_angle_esd> </PDBx:chem_link_angle> </PDBx:chem_link_angleCategory> This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. The standard uncertainty (estimated standard deviation) of attribute value_angle in category chem_link_angle. The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by attribute atom_id_1 in category chem_comp_angle and attribute atom_id_3 in category chem_comp_angle. The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_comp_angle. The ID of the first of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_1_comp_id) in category chem_comp_angle. The ID of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_2_comp_id) in category chem_comp_angle. The ID of the third of the three atoms that define the angle. An atom with this ID must exist in the component of the type specified by attribute type_comp_1 in category chem_comp_link (or attribute type_comp_2 in category chem_comp_link, where the appropriate data item is indicated by the value of attribute atom_3_comp_id) in category chem_comp_angle. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure. Example 1 - Engh & Huber parameters [Acta Cryst. (1991), A47, 392-400] as interpreted by J. P. Priestle (1995). Consistent Stereochemical Dictionaries for Refinement and Model Building. CCP4 Daresbury Study Weekend, DL-CONF-95-001, ISSN 1358-6254. Warrington: Daresbury Laboratory. <PDBx:chem_link_bondCategory> <PDBx:chem_link_bond atom_id_1="N" atom_id_2="CA" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.458</PDBx:value_dist> <PDBx:value_dist_esd>0.019</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="CA" atom_id_2="C" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.525</PDBx:value_dist> <PDBx:value_dist_esd>0.021</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="C" atom_id_2="N" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>2</PDBx:atom_2_comp_id> <PDBx:value_dist>1.329</PDBx:value_dist> <PDBx:value_dist_esd>0.014</PDBx:value_dist_esd> </PDBx:chem_link_bond> <PDBx:chem_link_bond atom_id_1="C" atom_id_2="O" link_id="PEPTIDE"> <PDBx:atom_1_comp_id>1</PDBx:atom_1_comp_id> <PDBx:atom_2_comp_id>1</PDBx:atom_2_comp_id> <PDBx:value_dist>1.231</PDBx:value_dist> <PDBx:value_dist_esd>0.020</PDBx:value_dist_esd> </PDBx:chem_link_bond> </PDBx:chem_link_bondCategory> This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the link. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. The standard uncertainty (estimated standard deviation) of attribute value_dist in category chem_link_bond. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. The ID of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The ID of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category. This data item indicates whether the chiral atom is found in the first or the second of the two components connected by the link. The chiral configuration of the atom that is a chiral centre. The ID of the atom that is a chiral centre. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The total number of atoms bonded to the atom specified by attribute atom_id in category chem_link_chir. The number of non-hydrogen atoms bonded to the atom specified by attribute atom_id in category chem_link_chir. A flag to indicate whether a chiral volume should match the standard value in both magnitude and sign, or in magnitude only. The chiral volume, V(c), for chiral centres that involve a chiral atom bonded to three non-hydrogen atoms and one hydrogen atom. V~c~ = V1 * (V2 X V3) V1 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the first atom in the CHEM_LINK_CHIR_ATOM list V2 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the second atom in the CHEM_LINK_CHIR_ATOM list V3 = the vector distance from the atom specified by attribute atom_id in category chem_link_chir to the third atom in the CHEM_LINK_CHIR_ATOM list * = the vector dot product X = the vector cross product The standard uncertainty (estimated standard deviation) of attribute volume_three in category chem_link_chir. The value of attribute id in category chem_link_chir must uniquely identify a record in the CHEM_LINK_CHIR list. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components. This data item indicates whether the atom bonded to a chiral atom is found in the first or the second of the two components connected by the link. The standard uncertainty (estimated standard deviation) of the position of this atom from the plane defined by all of the atoms in the plane. The ID of an atom bonded to the chiral atom. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. This data item is a pointer to attribute id in category chem_link_chir in the CHEM_LINK_CHIR category. Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category. The total number of atoms in the plane. The number of non-hydrogen atoms in the plane. The value of attribute id in category chem_link_plane must uniquely identify a record in the CHEM_LINK_PLANE list. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components. This data item indicates whether the atom in a plane is found in the first or the second of the two components connected by the link. The ID of an atom involved in the plane. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. This data item is a pointer to attribute id in category chem_link_plane in the CHEM_LINK_PLANE category. Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category. This data item indicates whether atom 1 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 2 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 3 is found in the first or the second of the two components connected by the link. This data item indicates whether atom 4 is found in the first or the second of the two components connected by the link. The ID of the first of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The ID of the second of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The ID of the third of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The ID of the fourth of the four atoms that define the torsion angle. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. The value of attribute id in category chem_link_tor must uniquely identify a record in the CHEM_LINK_TOR list. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both. A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed in degrees. The standard uncertainty (estimated standard deviation) of attribute angle in category chem_link_tor_value. A value that should be taken as a potential target value for the torsion angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_link_tor.atom_id_1 and _chem_link_tor.atom_id_4 in the referenced record in the CHEM_LINK_TOR list. Note that the torsion angle cannot be fully specified by a distance (for instance, a torsion angle of -60 degree will yield the same distance as a 60 degree angle). However, the distance specification can be useful for refinement in situations in which the angle is already close to the desired value. The standard uncertainty (estimated standard deviation) of attribute dist in category chem_link_tor_value. This data item is a pointer to attribute id in category chem_link_tor in the CHEM_LINK_TOR category. Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values. Example 1 - based on data set 9597gaus of Alyea, Ferguson & Kannan [Acta Cryst. (1996), C52, 765-767]. <PDBx:chemicalCategory> <PDBx:chemical entry_id="9597gaus"> <PDBx:name_systematic>trans-bis(tricyclohexylphosphine)tetracarbonylmolybdenum(0)</PDBx:name_systematic> </PDBx:chemical> </PDBx:chemicalCategory> Necessary conditions for the assignment of attribute absolute_configuration in category chemical are given by H. D. Flack and G. Bernardinelli (1999, 2000). Ref: Flack, H. D. & Bernardinelli, G. (1999). Acta Cryst. A55, 908-915. (http://www.iucr.org/paper?sh0129) Flack, H. D. & Bernardinelli, G. (2000). J. Appl. Cryst. 33, 1143-1148. (http://www.iucr.org/paper?ks0021) Description of the source of the compound under study, or of the parent molecule if a simple derivative is studied. This includes the place of discovery for minerals or the actual source of a natural product. From Norilsk (USSR) Extracted from the bark of Cinchona Naturalis The temperature in kelvins at which the crystalline solid changes to a liquid. A temperature in kelvins above which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. attribute melting_point in category chemical should always be used in preference to these two items whenever possible. A temperature in kelvins below which the melting point (the temperature at which the crystalline solid changes to a liquid) lies. _chemical.melting_point_gt and _chemical.melting_point_lt allow a range of temperatures to be given. attribute melting_point in category chemical should always be used in preference to these two items whenever possible. Trivial name by which the compound is commonly known. 1-bromoestradiol Mineral name accepted by the International Mineralogical Association. Use only for natural minerals. See also attribute compound_source in category chemical. chalcopyrite Commonly used structure-type name. Usually only applied to minerals or inorganic compounds. perovskite sphalerite A15 IUPAC or Chemical Abstracts full name of the compound. 1-bromoestra-1,3,5(10)-triene-3,17\b-diol The optical rotation in solution of the compound is specified in the following format: '[\a]^TEMP^~WAVE~ = SORT (c = CONC, SOLV)' where: TEMP is the temperature of the measurement in degrees Celsius, WAVE is an indication of the wavelength of the light used for the measurement, CONC is the concentration of the solution given as the mass of the substance in g in 100 ml of solution, SORT is the signed value (preceded by a + or a - sign) of 100.\a/(l.c), where \a is the signed optical rotation in degrees measured in a cell of length l in dm and c is the value of CONC as defined above, and SOLV is the chemical formula of the solvent. [\a]^25^~D~ = +108 (c = 3.42, CHCl~3~) A free-text description of the biological properties of the material. diverse biological activities including use as a laxative and strong antibacterial activity against S. aureus and weak activity against cyclooxygenase-1 (COX-1) antibiotic activity against Bacillus subtilis (ATCC 6051) but no significant activity against Candida albicans (ATCC 14053), Aspergillus flavus (NRRL 6541) and Fusarium verticillioides (NRRL 25457) weakly potent lipoxygenase nonredox inhibitor no influenza A virus sialidase inhibitory and plaque reduction activities low toxicity against Drosophila melanogaster A free-text description of the physical properties of the material. air-sensitive moisture-sensitive hygroscopic deliquescent oxygen-sensitive photo-sensitive pyrophoric semiconductor ferromagnetic at low temperature paramagnetic and thermochromic The temperature in kelvins at which the solid decomposes. 350 The estimated standard deviation of attribute temperature_decomposition in category chemical. A temperature in kelvins above which the solid is known to decompose. attribute temperature_decomposition_gt in category chemical and attribute temperature_decomposition_lt in category chemical allow a range of temperatures to be given. attribute temperature_decomposition in category chemical should always be used in preference to these two items whenever possible. 350 A temperature in kelvins below which the solid is known to decompose. attribute temperature_decomposition_gt in category chemical and attribute temperature_decomposition_lt in category chemical allow a range of temperatures to be given. attribute temperature_decomposition in category chemical should always be used in preference to these two items whenever possible. 350 The temperature in kelvins at which the solid sublimes. 350 The estimated standard deviation of attribute temperature_sublimation in category chemical. A temperature in kelvins above which the solid is known to sublime. attribute temperature_sublimation_gt in category chemical and attribute temperature_sublimation_lt in category chemical allow a range of temperatures to be given. attribute temperature_sublimation in category chemical should always be used in preference to these two items whenever possible. 350 A temperature in kelvins below which the solid is known to sublime. attribute temperature_sublimation_gt in category chemical and attribute temperature_sublimation_lt in category chemical allow a range of temperatures to be given. attribute temperature_sublimation in category chemical should always be used in preference to these two items whenever possible. 350 This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity. Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. <PDBx:chemical_conn_atomCategory> <PDBx:chemical_conn_atom number="1"> <PDBx:NCA>1</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.39</PDBx:display_x> <PDBx:display_y>.81</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="2"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.39</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="3"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.14</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="4"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.33</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="5"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.11</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="6"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.03</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="7"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.03</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="8"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.11</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="9"> <PDBx:NCA>1</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.54</PDBx:display_x> <PDBx:display_y>.81</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="10"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.54</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>S</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="11"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.80</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="12"> <PDBx:NCA>3</PDBx:NCA> <PDBx:NH>0</PDBx:NH> <PDBx:display_x>.60</PDBx:display_x> <PDBx:display_y>.88</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="13"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.84</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="14"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.91</PDBx:display_x> <PDBx:display_y>.96</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="15"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.91</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> <PDBx:chemical_conn_atom number="16"> <PDBx:NCA>2</PDBx:NCA> <PDBx:NH>2</PDBx:NH> <PDBx:display_x>.84</PDBx:display_x> <PDBx:display_y>.80</PDBx:display_y> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:chemical_conn_atom> </PDBx:chemical_conn_atomCategory> The number of connected atoms excluding terminal hydrogen atoms. The total number of hydrogen atoms attached to this atom, regardless of whether they are included in the refinement or the ATOM_SITE list. This number is the same as attribute attached_hydrogens in category atom_site only if none of the hydrogen atoms appear in the ATOM_SITE list. The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 The 2D Cartesian x coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. The 2D Cartesian y coordinate of the position of this atom in a recognizable chemical diagram. The coordinate origin is at the lower left corner, the x axis is horizontal and the y axis is vertical. The coordinates must lie in the range 0.0 to 1.0. These coordinates can be obtained from projections of a suitable uncluttered view of the molecular structure. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. The chemical sequence number to be associated with this atom. Within an ATOM_SITE list, this number must match one of the attribute chemical_conn_number in category atom_site values. Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms. Example 1 - based on data set DPTD of Yamin, Suwandi, Fun, Sivakumar & bin Shawkataly [Acta Cryst. (1996), C52, 951-953]. <PDBx:chemical_conn_bondCategory> <PDBx:chemical_conn_bond atom_1="4" atom_2="1"> <PDBx:type>doub</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="4" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="4" atom_2="2"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="5" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="6" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="7" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="8" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="8" atom_2="3"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="10" atom_2="2"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="9"> <PDBx:type>doub</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="12" atom_2="10"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="13" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="14" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="15" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="16" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="16" atom_2="11"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="17" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="18" atom_2="5"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="19" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="20" atom_2="6"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="21" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="22" atom_2="7"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="23" atom_2="8"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="24" atom_2="8"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="25" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="26" atom_2="13"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="27" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="28" atom_2="14"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="29" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="30" atom_2="15"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="31" atom_2="16"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> <PDBx:chemical_conn_bond atom_1="32" atom_2="16"> <PDBx:type>sing</PDBx:type> </PDBx:chemical_conn_bond> </PDBx:chemical_conn_bondCategory> The chemical bond type associated with the connection between the two sites attribute atom_1 in category chemical_conn_bond and attribute atom_2 in category chemical_conn_bond. This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. This data item is a pointer to attribute number in category chemical_conn_atom in the CHEMICAL_CONN_ATOM category. Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and attribute sum in category chemical_formula. For the data item attribute moiety in category chemical_formula, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see attribute moiety). in category chemical_formula (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for attribute moiety in category chemical_formula formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in attribute structural in category chemical_formula, the order of the elements within any group or moiety should be: C, then H, then the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:chemical_formulaCategory> <PDBx:chemical_formula entry_id="TOZ"> <PDBx:moiety>C18 H25 N O3</PDBx:moiety> <PDBx:sum>C18 H25 N O3</PDBx:sum> <PDBx:weight>303.40</PDBx:weight> </PDBx:chemical_formula> </PDBx:chemical_formulaCategory> Formula determined by standard chemical analysis including trace elements. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. Parentheses are used only for standard uncertainties (estimated standard deviations). Fe2.45(2) Ni1.60(3) S4 Formula expressed in conformance with IUPAC rules for inorganic and metal-organic compounds where these conflict with the rules for any other CHEMICAL_FORMULA entries. Typically used for formatting a formula in accordance with journal rules. This should appear in the data block in addition to the most appropriate of the other CHEMICAL_FORMULA data names. Ref: IUPAC (1990). Nomenclature of Inorganic Chemistry. Oxford: Blackwell Scientific Publications. [Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H Formula with each discrete bonded residue or ion shown as a separate moiety. See the CHEMICAL_FORMULA category description for rules for writing chemical formulae. In addition to the general formulae requirements, the following rules apply: (1) Moieties are separated by commas ','. (2) The order of elements within a moiety follows general rule (5) in the CHEMICAL_FORMULA category description. (3) Parentheses are not used within moieties but may surround a moiety. Parentheses may not be nested. (4) Charges should be placed at the end of the moiety. The charge '+' or '-' may be preceded by a numerical multiplier and should be separated from the last (element symbol + count) by a space. Pre- or post-multipliers may be used for individual moieties. C7 H4 Cl Hg N O3 S C12 H17 N4 O S 1+, C6 H2 N3 O7 1- C12 H16 N2 O6, 5(H2 O1) (Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O) See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae for inorganics, organometallics, metal complexes etc., in which bonded groups are preserved as discrete entities within parentheses, with post-multipliers as required. The order of the elements should give as much information as possible about the chemical structure. Parentheses may be used and nested as required. This formula should correspond to the structure as actually reported, i.e. trace elements not included in atom-type and atom-site data should not be included in this formula (see also attribute analytical) in category chemical_formula. Ca ((Cl O3)2 O)2 (H2 O)6 (Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2 See the CHEMICAL_FORMULA category description for the rules for writing chemical formulae in which all discrete bonded residues and ions are summed over the constituent elements, following the ordering given in general rule (5) in the CHEMICAL_FORMULA category description. Parentheses are not normally used. C18 H19 N7 O8 S Formula mass in daltons. This mass should correspond to the formulae given under attribute structural, in category chemical_formula _chemical_formula.moiety or _chemical_formula.sum and, together with the Z value and cell parameters, should yield the density given as attribute density_diffrn in category exptl_crystal. Formula mass in daltons measured by a non-diffraction experiment. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:citationCategory> <PDBx:citation id="primary"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>yes</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> The publication that directly relates to this coordinate set.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>265</PDBx:journal_volume> <PDBx:page_first>14209</PDBx:page_first> <PDBx:page_last>14219</PDBx:page_last> <PDBx:title> Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-Angstroms resolution.</PDBx:title> <PDBx:year>1990</PDBx:year> </PDBx:citation> <PDBx:citation id="2"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>UK</PDBx:country> <PDBx:details> Determination of the structure of the unliganded enzyme.</PDBx:details> <PDBx:journal_abbrev>Nature</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>NATUAS</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>006</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0028-0836</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>337</PDBx:journal_volume> <PDBx:page_first>615</PDBx:page_first> <PDBx:page_last>619</PDBx:page_last> <PDBx:title> Three-dimensional structure of aspartyl-protease from human immunodeficiency virus HIV-1.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> <PDBx:citation id="3"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> Crystallization of the unliganded enzyme.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>264</PDBx:journal_volume> <PDBx:page_first>1919</PDBx:page_first> <PDBx:page_last>1921</PDBx:page_last> <PDBx:title> Crystallization of the aspartylprotease from human immunodeficiency virus, HIV-1.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> <PDBx:citation id="4"> <PDBx:book_id_ISBN xsi:nil="true" /> <PDBx:book_publisher xsi:nil="true" /> <PDBx:book_title xsi:nil="true" /> <PDBx:coordinate_linkage>no</PDBx:coordinate_linkage> <PDBx:country>US</PDBx:country> <PDBx:details> Expression and purification of the enzyme.</PDBx:details> <PDBx:journal_abbrev>J. Biol. Chem.</PDBx:journal_abbrev> <PDBx:journal_id_ASTM>HBCHA3</PDBx:journal_id_ASTM> <PDBx:journal_id_CSD>071</PDBx:journal_id_CSD> <PDBx:journal_id_ISSN>0021-9258</PDBx:journal_id_ISSN> <PDBx:journal_issue xsi:nil="true" /> <PDBx:journal_volume>264</PDBx:journal_volume> <PDBx:page_first>2307</PDBx:page_first> <PDBx:page_last>2312</PDBx:page_last> <PDBx:title> Human immunodeficiency virus protease. Bacterial expression and characterization of the purified aspartic protease.</PDBx:title> <PDBx:year>1989</PDBx:year> </PDBx:citation> </PDBx:citationCategory> Abstract for the citation. This is used most when the citation is extracted from a bibliographic database that contains full text or abstract information. The Chemical Abstracts Service (CAS) abstract identifier; relevant for journal articles. The International Standard Book Number (ISBN) code assigned to the book cited; relevant for books or book chapters. The name of the publisher of the citation; relevant for books or book chapters. John Wiley and Sons The location of the publisher of the citation; relevant for books or book chapters. London The title of the book in which the citation appeared; relevant for books or book chapters. attribute coordinate_linkage in category citation states whether this citation is concerned with precisely the set of coordinates given in the data block. If, for instance, the publication described the same structure, but the coordinates had undergone further refinement prior to the creation of the data block, the value of this data item would be 'no'. The country/region of publication; relevant for books and book chapters. Identifier ('refcode') of the database record in the Cambridge Structural Database that contains details of the cited structure. LEKKUH Accession number used by Medline to categorize a specific bibliographic entry. 89064067 A description of special aspects of the relationship of the contents of the data block to the literature item cited. citation relates to this precise coordinate set citation relates to earlier low-resolution structure citation relates to further refinement of structure reported in citation 2 Abbreviated name of the cited journal as given in the Chemical Abstracts Service Source Index. J. Mol. Biol. Full name of the cited journal; relevant for journal articles. Journal of Molecular Biology The American Society for Testing and Materials (ASTM) code assigned to the journal cited (also referred to as the CODEN designator of the Chemical Abstracts Service); relevant for journal articles. The Cambridge Structural Database (CSD) code assigned to the journal cited; relevant for journal articles. This is also the system used at the Protein Data Bank (PDB). 0070 The International Standard Serial Number (ISSN) code assigned to the journal cited; relevant for journal articles. Issue number of the journal cited; relevant for journal articles. 2 Volume number of the journal cited; relevant for journal articles. 174 Language in which the cited article is written. German The first page of the citation; relevant for journal articles, books and book chapters. The last page of the citation; relevant for journal articles, books and book chapters. Document Object Identifier used by doi.org to uniquely specify bibliographic entry. 10.2345/S1384107697000225 Ascession number used by PubMed to categorize a specific bibliographic entry. 12627512 If citation is a patent, the accession issued by a patent office. The title of the citation; relevant for journal articles, books and book chapters. Structure of diferric duck ovotransferrin at 2.35 Angstroms resolution. Flag to indicate that this citation will not be published. The year of the citation; relevant for journal articles, books and book chapters. 1984 The value of attribute id in category citation must uniquely identify a record in the CITATION list. The attribute id in category citation 'primary' should be used to indicate the citation that the author(s) consider to be the most pertinent to the contents of the data block. Note that this item need not be a number; it can be any unique identifier. primary 1 2 Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:citation_authorCategory> <PDBx:citation_author citation_id="primary" name="Fitzgerald, P.M.D." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="McKeever, B.M." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Van Middlesworth, J.F." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Springer, J.P." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Leu, C.-T." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Herber, W.K." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Dixon, R.A.F." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="primary" name="Darke, P.L." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Navia, M.A." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Fitzgerald, P.M.D." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="McKeever, B.M." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Leu, C.-T." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Heimbach, J.C." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Herber, W.K." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Sigal, I.S." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Darke, P.L." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="2" name="Springer, J.P." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="McKeever, B.M." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Navia, M.A." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Fitzgerald, P.M.D." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Springer, J.P." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Leu, C.-T." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Heimbach, J.C." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Herber, W.K." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Sigal, I.S." ordinal="8"></PDBx:citation_author> <PDBx:citation_author citation_id="3" name="Darke, P.L." ordinal="9"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Darke, P.L." ordinal="1"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Leu, C.-T." ordinal="2"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Davis, L.J." ordinal="3"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Heimbach, J.C." ordinal="4"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Diehl, R.E." ordinal="5"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Hill, W.S." ordinal="6"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Dixon, R.A.F." ordinal="7"></PDBx:citation_author> <PDBx:citation_author citation_id="4" name="Sigal, I.S." ordinal="8"></PDBx:citation_author> </PDBx:citation_authorCategory> The Open Researcher and Contributor ID (ORCID). 0000-0002-6681-547X This data item is a pointer to attribute id in category citation in the CITATION category. Name of an author of the citation; relevant for journal articles, books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A This data item defines the order of the author's name in the list of authors of a citation. Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list. Example 1 - hypothetical example. <PDBx:citation_editorCategory> <PDBx:citation_editor citation_id="5" name="McKeever, B.M."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Navia, M.A."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Fitzgerald, P.M.D."></PDBx:citation_editor> <PDBx:citation_editor citation_id="5" name="Springer, J.P."></PDBx:citation_editor> </PDBx:citation_editorCategory> This data item defines the order of the editor's name in the list of editors of a citation. This data item is a pointer to attribute id in category citation in the CITATION category. Names of an editor of the citation; relevant for books and book chapters. The family name(s), followed by a comma and including any dynastic components, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows a more detailed description of computer programs and their attributes to be given, would be used instead. Example 1 - Rodr\'iguez-Romera, Ruiz-P\'erez & Solans [Acta Cryst. (1996), C52, 1415-1417]. <PDBx:computingCategory> <PDBx:computing entry_id="1ABC"> <PDBx:cell_refinement>CAD-4 (Enraf-Nonius, 1989)</PDBx:cell_refinement> <PDBx:data_collection>CAD-4 (Enraf-Nonius, 1989)</PDBx:data_collection> <PDBx:data_reduction>CFEO (Solans, 1978)</PDBx:data_reduction> <PDBx:molecular_graphics>ORTEPII (Johnson, 1976)</PDBx:molecular_graphics> <PDBx:publication_material>PARST (Nardelli, 1983)</PDBx:publication_material> <PDBx:structure_refinement>SHELXL93 (Sheldrick, 1993)</PDBx:structure_refinement> <PDBx:structure_solution>SHELXS86 (Sheldrick, 1990)</PDBx:structure_solution> </PDBx:computing> </PDBx:computingCategory> Software used for cell refinement. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989) Software used for data collection. Give the program or package name and a brief reference. CAD4 (Enraf-Nonius, 1989) Software used for data reduction. Give the program or package name and a brief reference. DIFDAT, SORTRF, ADDREF (Hall & Stewart, 1990) Software used for molecular graphics. Give the program or package name and a brief reference. FRODO (Jones, 1986), ORTEP (Johnson, 1965) Program/package name for data reduction/data scaling Program/package name for data reduction/intensity integration software Program/package name for structure refinement method. Software used for generating material for publication. Give the program or package name and a brief reference. Software used for refinement of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) X-PLOR (Brunger, 1992) Software used for solution of the structure. Give the program or package name and a brief reference. SHELX85 (Sheldrick, 1985) This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older CIFs. A history of changes made by the Cambridge Crystallographic Data Centre and incorporated into the Cambridge Structural Database (CSD). The code assigned by Chemical Abstracts. The code assigned by the Cambridge Structural Database. The code assigned by the Inorganic Crystal Structure Database. The code assigned by the Metals Data File. The code assigned by the NBS (NIST) Crystal Data Database. The code assigned by the Protein Data Bank. The code assigned by the Powder Diffraction File (JCPDS/ICDD). Deposition numbers assigned by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC. Deposition numbers assigned by the Fachinformationszentrum Karlsruhe (FIZ) to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). Deposition numbers assigned by various journals to files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). The ASTM CODEN designator for a journal as given in the Chemical Source List maintained by the Chemical Abstracts Service. The journal code used in the Cambridge Structural Database. The code assigned by the NDB. BDL001 The code assigned by the PDB. 1BNA The codes of related PDB entries. 1NK1,1NK2 This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_2Category> <PDBx:database_2 database_code="5HVP" database_id="PDB"></PDBx:database_2> </PDBx:database_2Category> Document Object Identifier (DOI) for this entry registered with http://crossref.org. 10.2210/pdb6lu7/pdb Extended accession code issued for for attribute database_code in category database_2 assigned by the database identified in attribute database_id in category database_2. pdb_00006lu7 The code assigned by the database identified in attribute database_id in category database_2. 1ABC ABCDEF An abbreviation that identifies the database. Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. Example 1 - hypothetical example. <PDBx:database_PDB_caveatCategory> <PDBx:database_PDB_caveat id="1"> <PDBx:text> THE CRYSTAL TRANSFORMATION IS IN ERROR BUT IS</PDBx:text> </PDBx:database_PDB_caveat> <PDBx:database_PDB_caveat id="2"> <PDBx:text> UNCORRECTABLE AT THIS TIME</PDBx:text> </PDBx:database_PDB_caveat> </PDBx:database_PDB_caveatCategory> The full text of the PDB caveat record. A unique identifier for the PDB caveat record. The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. The [1][1] element of the PDB ORIGX matrix. The [1][2] element of the PDB ORIGX matrix. The [1][3] element of the PDB ORIGX matrix. The [2][1] element of the PDB ORIGX matrix. The [2][2] element of the PDB ORIGX matrix. The [2][3] element of the PDB ORIGX matrix. The [3][1] element of the PDB ORIGX matrix. The [3][2] element of the PDB ORIGX matrix. The [3][3] element of the PDB ORIGX matrix. The [1] element of the PDB ORIGX vector. The [2] element of the PDB ORIGX vector. The [3] element of the PDB ORIGX vector. The [1][1] element of the PDB SCALE matrix. The [1][2] element of the PDB SCALE matrix. The [1][3] element of the PDB SCALE matrix. The [2][1] element of the PDB SCALE matrix. The [2][2] element of the PDB SCALE matrix. The [2][3] element of the PDB SCALE matrix. The [3][1] element of the PDB SCALE matrix. The [3][2] element of the PDB SCALE matrix. The [3][3] element of the PDB SCALE matrix. The [1] element of the PDB SCALE vector. The [2] element of the PDB SCALE vector. The [3] element of the PDB SCALE vector. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. NOTE: These remark records in this category are not uniformly annotated by the PDB and may not be consistent with nomenclature or labeling used in the entry. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_PDB_remarkCategory> <PDBx:database_PDB_remark id="3"> <PDBx:text> REFINEMENT. BY THE RESTRAINED LEAST-SQUARES PROCEDURE OF J. KONNERT AND W. HENDRICKSON (PROGRAM *PROLSQ*). THE R VALUE IS 0.176 FOR 12901 REFLECTIONS IN THE RESOLUTION RANGE 8.0 TO 2.0 ANGSTROMS WITH I .GT. SIGMA(I). RMS DEVIATIONS FROM IDEAL VALUES (THE VALUES OF SIGMA, IN PARENTHESES, ARE THE INPUT ESTIMATED STANDARD DEVIATIONS THAT DETERMINE THE RELATIVE WEIGHTS OF THE CORRESPONDING RESTRAINTS) DISTANCE RESTRAINTS (ANGSTROMS) BOND DISTANCE 0.018(0.020) ANGLE DISTANCE 0.038(0.030) PLANAR 1-4 DISTANCE 0.043(0.040) PLANE RESTRAINT (ANGSTROMS) 0.015(0.020) CHIRAL-CENTER RESTRAINT (ANGSTROMS**3) 0.177(0.150) NON-BONDED CONTACT RESTRAINTS (ANGSTROMS) SINGLE TORSION CONTACT 0.216(0.500) MULTIPLE TORSION CONTACT 0.207(0.500) POSSIBLE HYDROGEN BOND 0.245(0.500) CONFORMATIONAL TORSION ANGLE RESTRAINT (DEGREES) PLANAR (OMEGA) 2.6(3.0) STAGGERED 17.4(15.0) ORTHONORMAL 18.1(20.0)</PDBx:text> </PDBx:database_PDB_remark> <PDBx:database_PDB_remark id="4"> <PDBx:text> THE TWO CHAINS OF THE DIMERIC ENZYME HAS BEEN ASSIGNED THE CHAIN INDICATORS *A* AND *B*.</PDBx:text> </PDBx:database_PDB_remark> </PDBx:database_PDB_remarkCategory> The full text of the PDB remark record. A unique identifier for the PDB remark record. Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:database_PDB_revCategory> <PDBx:database_PDB_rev num="1"> <PDBx:author_name>Fitzgerald, Paula M.D</PDBx:author_name> <PDBx:date>1991-10-15</PDBx:date> <PDBx:date_original>1990-04-30</PDBx:date_original> <PDBx:mod_type>0</PDBx:mod_type> <PDBx:status>full release</PDBx:status> </PDBx:database_PDB_rev> </PDBx:database_PDB_revCategory> The name of the person responsible for submitting this revision to the PDB. The family name(s) followed by a comma precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Date the PDB revision took place. Taken from the REVDAT record. Date the entry first entered the PDB database in the form yyyy-mm-dd. Taken from the PDB HEADER record. 1980-08-21 A code taken from the REVDAT record classifying common types of entry revisions. The first PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE The second PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE The third PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE The fourth PDB record name that was revised. OBSOLETE LOCAL ITEM -- Replaced by attribute type in category database_PDB_rev_record TITLE HEADER COMPND SOURCE The PDB code for a subsequent PDB entry that replaced the PDB file corresponding to this data block. The PDB code for a previous PDB entry that was replaced by the PDB file corresponding to this data block. The status of this revision. The value of attribute num in category database_PDB_rev must uniquely and sequentially identify a record in the DATABASE_PDB_REV list. Note that this item must be a number and that modification numbers are assigned in increasing numerical order. Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source. Example 1 - hypothetical example. <PDBx:database_PDB_rev_recordCategory> <PDBx:database_PDB_rev_record rev_num="1" type="CONECT"> <PDBx:details> Error fix - incorrect connection between atoms 2312 and 2317</PDBx:details> </PDBx:database_PDB_rev_record> <PDBx:database_PDB_rev_record rev_num="2" type="MATRIX"> <PDBx:details>For consistency with 1995-08-04 style-guide</PDBx:details> </PDBx:database_PDB_rev_record> <PDBx:database_PDB_rev_record rev_num="3" type="ORIGX"> <PDBx:details>Based on new data from author</PDBx:details> </PDBx:database_PDB_rev_record> </PDBx:database_PDB_rev_recordCategory> A description of special aspects of the revision of records in this PDB entry. Based on new data from author For consistency with 1995-08-04 style-guide For consistency with structural class This data item is a pointer to attribute num in category database_PDB_rev in the DATABASE_PDB_REV category. The types of records that were changed in this revision to a PDB entry. CRYST1 SCALE MTRIX ATOM HETATM The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if the data block was created by reformatting a PDB format file. A description of special aspects of this TVECT. The [1] element of the PDB TVECT vector. The [2] element of the PDB TVECT vector. The [3] element of the PDB TVECT vector. The value of attribute id in category database_PDB_tvect must uniquely identify a record in the DATABASE_PDB_TVECT list. Note that this item need not be a number; it can be any unique identifier. Data items in the DIFFRN category record details about the diffraction data and their measurement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrnCategory> <PDBx:diffrn id="Set1"> <PDBx:ambient_environment> Mother liquor from the reservoir of the vapor diffusion experiment, mounted in room air</PDBx:ambient_environment> <PDBx:ambient_temp>293.0</PDBx:ambient_temp> <PDBx:crystal_support> 0.7 mm glass capillary, sealed with dental wax</PDBx:crystal_support> <PDBx:crystal_treatment> Equilibrated in rotating anode radiation enclosure for 18 hours prior to beginning of data collection</PDBx:crystal_treatment> </PDBx:diffrn> </PDBx:diffrnCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [(1991). Acta Cryst. C47, 2276-2277]. <PDBx:diffrnCategory> <PDBx:diffrn id="d1"> <PDBx:ambient_temp>293</PDBx:ambient_temp> <PDBx:details> \q scan width (1.0 + 0.14tan\q)\&#37;, \q scan rate 1.2\&#37; per min. Background counts for 5 sec on each side every scan.</PDBx:details> </PDBx:diffrn> </PDBx:diffrnCategory> The gas or liquid surrounding the sample, if not air. The mean hydrostatic pressure in kilopascals at which the intensities were measured. The estimated standard deviation of attribute ambient_pressure in category diffrn. The mean hydrostatic pressure in kilopascals above which the intensities were measured. attribute ambient_pressure_gt in category diffrn and attribute ambient_pressure_lt in category diffrn allow a pressure range to be given. attribute ambient_pressure in category diffrn should always be used in preference to these two items whenever possible. The mean hydrostatic pressure in kilopascals below which the intensities were measured. attribute ambient_pressure_gt in category diffrn and attribute ambient_pressure_lt in category diffrn allow a pressure range to be given. attribute ambient_pressure in category diffrn should always be used in preference to these two items whenever possible. The mean temperature in kelvins at which the intensities were measured. A description of special aspects of temperature control during data collection. The standard uncertainty (estimated standard deviation) of attribute ambient_temp in category diffrn. The mean temperature in kelvins above which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. attribute ambient_temp in category diffrn should always be used in preference to these two items whenever possible. The mean temperature in kelvins below which the intensities were measured. _diffrn.ambient_temp_gt and _diffrn.ambient_temp_lt allow a range of temperatures to be given. attribute ambient_temp in category diffrn should always be used in preference to these two items whenever possible. This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop Remarks about how the crystal was treated prior to intensity measurement. Particularly relevant when intensities were measured at low temperature. equilibrated in hutch for 24 hours flash frozen in liquid nitrogen slow cooled with direct air stream Special details of the diffraction measurement process. Should include information about source instability, crystal motion, degradation and so on. Y/N if using serial crystallography experiment in which multiple crystals contribute to each diffraction frame in the experiment. Y N This data item uniquely identifies a set of diffraction data. Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_attenuatorCategory> <PDBx:diffrn_attenuator code="1"> <PDBx:scale>16.976</PDBx:scale> </PDBx:diffrn_attenuator> </PDBx:diffrn_attenuatorCategory> Material from which the attenuator is made. The scale factor applied when an intensity measurement is reduced by an attenuator identified by attribute code. in category diffrn_attenuator The measured intensity must be multiplied by this scale to convert it to the same scale as unattenuated intensities. A code associated with a particular attenuator setting. This code is referenced by the attribute attenuator_code in category diffrn_refln which is stored with the diffraction data. See attribute scale in category diffrn_attenuator. Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_detectorCategory> <PDBx:diffrn_detector diffrn_id="d1"> <PDBx:detector>multiwire</PDBx:detector> <PDBx:type>Siemens</PDBx:type> </PDBx:diffrn_detector> </PDBx:diffrn_detectorCategory> The resolution of an area detector, in pixels/mm. A description of special aspects of the radiation detector. The general class of the radiation detector. photographic film scintillation counter CCD plate BF~3~ counter The deadtime in microseconds of the detector used to measure the diffraction intensities. The date of data collection. 1996-12-25 The total number of seconds required to measure this data set. 120.0 The total number of data frames collected for this data set. 20 100 The operating frequency of the detector (Hz) used in data collection. The make, model or name of the detector device used. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_measurementCategory> <PDBx:diffrn_measurement diffrn_id="d1"> <PDBx:details> 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees</PDBx:details> <PDBx:device>3-circle camera</PDBx:device> <PDBx:device_details>none</PDBx:device_details> <PDBx:device_type>Supper model x</PDBx:device_type> <PDBx:method>omega scan</PDBx:method> </PDBx:diffrn_measurement> </PDBx:diffrn_measurementCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_measurementCategory> <PDBx:diffrn_measurement diffrn_id="s1"> <PDBx:device_type>Philips PW1100/20 diffractometer</PDBx:device_type> <PDBx:method>\q/2\q</PDBx:method> </PDBx:diffrn_measurement> </PDBx:diffrn_measurementCategory> A description of special aspects of the intensity measurement. 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector angle 22.5 degrees The general class of goniometer or device used to support and orient the specimen. 3-circle camera 4-circle camera kappa-geometry camera oscillation camera precession camera A description of special aspects of the device used to measure the diffraction intensities. commercial goniometer modified locally to allow for 90\% \t arc The make, model or name of the measurement device (goniometer) used. Supper model q Huber model r Enraf-Nonius model s homemade Method used to measure intensities. profile data from theta/2theta scans The date of data measurement yyyy-mm-dd The physical device used to support the crystal during data collection. glass capillary quartz capillary fiber metal loop This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <PDBx:diffrn_orient_matrixCategory> <PDBx:diffrn_orient_matrix diffrn_id="set1"> <PDBx:UB11>-0.071479</PDBx:UB11> <PDBx:UB12>0.020208</PDBx:UB12> <PDBx:UB13>0.039076</PDBx:UB13> <PDBx:UB21>0.035372</PDBx:UB21> <PDBx:UB22>0.056209</PDBx:UB22> <PDBx:UB23>0.078324</PDBx:UB23> <PDBx:UB31>-0.007470</PDBx:UB31> <PDBx:UB32>0.067854</PDBx:UB32> <PDBx:UB33>-0.017832</PDBx:UB33> <PDBx:type> reciprocal axis matrix, multiplies hkl vector to generate diffractometer xyz vector and diffractometer angles</PDBx:type> </PDBx:diffrn_orient_matrix> </PDBx:diffrn_orient_matrixCategory> The [1][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [1][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [1][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [2][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [2][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [2][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [3][1] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [3][2] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. The [3][3] element of the 3x3 matrix that defines the dimensions of the reciprocal cell and its orientation with respect to the local diffractometer axes. See also attribute type in category diffrn_orient_matrix. A description of the orientation matrix type and how it should be applied to define the orientation of the crystal precisely with respect to the diffractometer axes. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <PDBx:diffrn_orient_reflnCategory> <PDBx:diffrn_orient_refln diffrn_id="myset1" index_h="2" index_k="0" index_l="2"> <PDBx:angle_chi>-28.45</PDBx:angle_chi> <PDBx:angle_kappa>-11.32</PDBx:angle_kappa> <PDBx:angle_omega>5.33</PDBx:angle_omega> <PDBx:angle_phi>101.78</PDBx:angle_phi> <PDBx:angle_psi>0.00</PDBx:angle_psi> <PDBx:angle_theta>10.66</PDBx:angle_theta> </PDBx:diffrn_orient_refln> </PDBx:diffrn_orient_reflnCategory> Diffractometer angle chi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle kappa of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle omega of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle phi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle psi of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. Diffractometer angle theta of a reflection used to define the orientation matrix in degrees. See attribute UB[][] in category diffrn_orient_matrix and the Miller indices in the DIFFRN_ORIENT_REFLN category. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Miller index h of a reflection used to define the orientation matrix. Miller index k of a reflection used to define the orientation matrix. Miller index l of a reflection used to define the orientation matrix. Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_radiationCategory> <PDBx:diffrn_radiation diffrn_id="set1"> <PDBx:collimation>0.3 mm double pinhole</PDBx:collimation> <PDBx:monochromator>graphite</PDBx:monochromator> <PDBx:type>Cu K\a</PDBx:type> <PDBx:wavelength_id>1</PDBx:wavelength_id> </PDBx:diffrn_radiation> </PDBx:diffrn_radiationCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_radiationCategory> <PDBx:diffrn_radiation diffrn_id="set1"> <PDBx:monochromator>graphite</PDBx:monochromator> <PDBx:type>Cu K\a</PDBx:type> <PDBx:wavelength_id>1</PDBx:wavelength_id> </PDBx:diffrn_radiation> </PDBx:diffrn_radiationCategory> The collimation or focusing applied to the radiation. 0.3 mm double-pinhole 0.5 mm focusing mirrors Absorption edge in angstroms of the radiation filter used. Half-width in millimetres of the incident beam in the direction perpendicular to the diffraction plane. The method used to obtain monochromatic radiation. If a mono- chromator crystal is used, the material and the indices of the Bragg reflection are specified. Zr filter Ge 220 none equatorial mounted graphite Indicates the method used to obtain monochromatic radiation. attribute monochromator in category diffrn_radiation describes the primary beam monochromator (pre-specimen monochromation). attribute pdbx_analyzer in category diffrn_radiation specifies the post-diffraction analyser (post-specimen) monochromation. Note that monochromators may have either 'parallel' or 'antiparallel' orientation. It is assumed that the geometry is parallel unless specified otherwise. In a parallel geometry, the position of the monochromator allows the incident beam and the final post-specimen and post-monochromator beam to be as close to parallel as possible. In a parallel geometry, the diffracting planes in the specimen and monochromator will be parallel when 2*theta(monochromator) is equal to 2*theta (specimen). For further discussion see R. Jenkins and R. Snyder, Introduction to X-ray Powder Diffraction, Wiley (1996), pp. 164-5. GE(111) Zr filter Ge 220 none equatorial mounted graphite (0001) Si (111), antiparallel SINGLE WAVELENGTH, LAUE, or MAD. SINGLE WAVELENGTH MONOCHROMATIC LAUE MAD OTHER Monochromatic or Laue. M L The radiation scattering type for this diffraction data set. Wavelength of radiation. Comma separated list of wavelengths or wavelength range. The angle in degrees, as viewed from the specimen, between the perpendicular component of the polarization and the diffraction plane. See attribute polarisn_ratio in category diffrn_radiation. Polarization ratio of the diffraction beam incident on the crystal. This is the ratio of the perpendicularly polarized to the parallel-polarized component of the radiation. The perpendicular component forms an angle of attribute polarisn_norm in category diffrn_radiation to the normal to the diffraction plane of the sample (i.e. the plane containing the incident and reflected beams). The nature of the radiation used (i.e. the name of the subatomic particle or the region of the electromagnetic spectrum). It is strongly recommended that this information is given, so that the probe radiation can be simply determined. The nature of the radiation. This is typically a description of the X-ray wavelength in Siegbahn notation. CuK\a Cu K\a~1~ Cu K-L~2,3~ white-beam This data item is a pointer to attribute id in category diffrn_radiation_wavelength in the DIFFRN_RADIATION_WAVELENGTH category. The IUPAC symbol for the X-ray wavelength for the probe radiation. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_radiation_wavelengthCategory> <PDBx:diffrn_radiation_wavelength id="1"> <PDBx:wavelength>1.54</PDBx:wavelength> <PDBx:wt>1.0</PDBx:wt> </PDBx:diffrn_radiation_wavelength> </PDBx:diffrn_radiation_wavelengthCategory> The radiation wavelength in angstroms. The relative weight of a wavelength identified by the code attribute id in category diffrn_radiation_wavelength in the list of wavelengths. The code identifying each value of attribute wavelength. in category diffrn_radiation_wavelength Items in the DIFFRN_RADIATION_WAVELENGTH category are looped when multiple wavelengths are used. This code is used to link with the DIFFRN_REFLN category. The attribute wavelength_id in category diffrn_refln codes must match one of the codes defined in this category. x1 x2 neut Data items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by attribute diffrn_id. in category diffrn_refln The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by attribute diffrn_id in category diffrn_reflns. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4 for data set 'set1' reflection 1102. <PDBx:diffrn_reflnCategory> <PDBx:diffrn_refln diffrn_id="set1" id="1102"> <PDBx:angle_chi>32.21</PDBx:angle_chi> <PDBx:angle_kappa>20.12</PDBx:angle_kappa> <PDBx:angle_omega>11.54</PDBx:angle_omega> <PDBx:angle_phi>176.02</PDBx:angle_phi> <PDBx:angle_psi>0.00</PDBx:angle_psi> <PDBx:angle_theta>23.08</PDBx:angle_theta> <PDBx:attenuator_code>Ni.005</PDBx:attenuator_code> <PDBx:counts_bg_1>22</PDBx:counts_bg_1> <PDBx:counts_bg_2>25</PDBx:counts_bg_2> <PDBx:counts_net>3450</PDBx:counts_net> <PDBx:counts_peak>321</PDBx:counts_peak> <PDBx:counts_total>3499</PDBx:counts_total> <PDBx:detect_slit_horiz>0.04</PDBx:detect_slit_horiz> <PDBx:detect_slit_vert>0.02</PDBx:detect_slit_vert> <PDBx:elapsed_time>1.00</PDBx:elapsed_time> <PDBx:index_h>4</PDBx:index_h> <PDBx:index_k>0</PDBx:index_k> <PDBx:index_l>2</PDBx:index_l> <PDBx:intensity_net>202.56</PDBx:intensity_net> <PDBx:intensity_sigma>2.18</PDBx:intensity_sigma> <PDBx:scale_group_code>A24</PDBx:scale_group_code> <PDBx:scan_mode>om</PDBx:scan_mode> <PDBx:scan_mode_backgd>mo</PDBx:scan_mode_backgd> <PDBx:scan_rate>1.2</PDBx:scan_rate> <PDBx:scan_time_backgd>900.00</PDBx:scan_time_backgd> <PDBx:scan_width>1.0</PDBx:scan_width> <PDBx:sint_over_lambda>0.25426</PDBx:sint_over_lambda> <PDBx:standard_code>1</PDBx:standard_code> <PDBx:wavelength>1.54184</PDBx:wavelength> <PDBx:wavelength_id>Cu1fixed</PDBx:wavelength_id> </PDBx:diffrn_refln> </PDBx:diffrn_reflnCategory> The diffractometer angle chi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle kappa of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle omega of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle phi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle psi of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The diffractometer angle theta of a reflection in degrees. This angle corresponds to the specified orientation matrix and the original measured cell before any subsequent cell transformations. The code identifying the attenuator setting for this reflection. This code must match one of the attribute code in category diffrn_attenuator values. The code identifying the class to which this reflection has been assigned. This code must match a value of attribute code in category diffrn_reflns_class. Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. The diffractometer counts for the measurement of the background before the peak. The diffractometer counts for the measurement of the background after the peak. The diffractometer counts for the measurement of net counts after background removal. The diffractometer counts for the measurement of counts for the peak scan or position. The diffractometer counts for the measurement of total counts (background plus peak). Total slit aperture in degrees in the diffraction plane. Total slit aperture in degrees perpendicular to the diffraction plane. Elapsed time in minutes from the start of the diffraction experiment to the measurement of this intensity. Miller index h of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. Miller index k of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. Miller index l of a reflection. The values of the Miller indices in the DIFFRN_REFLN category need not match the values of the Miller indices in the REFLN category if a transformation of the original measured cell has taken place. Details of the cell transformation are given in attribute reduction_process in category diffrn_reflns. See also attribute transf_matrix[][] in category diffrn_reflns. Net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. Standard uncertainty (estimated standard deviation) of the intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. Standard uncertainty of the net intensity calculated from the diffraction counts after the attenuator and standard scales have been applied. Detector coordinate (in pixels) along the X-direction for this reflection. This is often the position where the calculated reflection centroid is predicted to occur. The detector X-direction is most often along the fast changing array index of the 2D diffraction array, while the Y-coordinate is along the slow changing array index. Detector coordinate (in pixels) along the Y-direction for this reflection. This is often the position where the calculated reflection centroid is predicted to occur. The detector X-direction is most often along the fast changing array index of the 2D diffraction array, while the Y-coordinate is along the slow changing array index. The identifier of the diffraction image this reflection is associated with. This is often the image where the calculated reflection centroid is predicted to occur. The value of the angle around the scan axis for this reflection. This is often the scan angle at which the calculated reflection centroid is predicted to occur. The scale factor applied to an individual reflection intensity at the last scaling step before merging all measurements belonging to symmetry-unique reflections into a merged intensity. The value of the angle around the scan axis for this reflection. This is often the scan angle at which the calculated reflection centroid is predicted to occur. The code identifying the scale applying to this reflection. This data item is a pointer to attribute code in category diffrn_scale_group in the DIFFRN_SCALE_GROUP category. The code identifying the mode of scanning for measurements using a diffractometer. See _diffrn_refln.scan_width and _diffrn_refln.scan_mode_backgd. The code identifying the mode of scanning a reflection to measure the background intensity. The rate of scanning a reflection in degrees per minute to measure the intensity. The time spent measuring each background in seconds. The scan width in degrees of the scan mode defined by the code attribute scan_mode in category diffrn_refln. The (sin theta)/lambda value in reciprocal angstroms for this reflection. The code identifying that this reflection was measured as a standard intensity. This data item is a pointer to attribute code in category diffrn_standard_refln in the DIFFRN_STANDARD_REFLN category. The mean wavelength in angstroms of the radiation used to measure the intensity of this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. This data item is a pointer to attribute wavelength_id in category diffrn_radiation in the DIFFRN_RADIATION category. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. The value of attribute id in category diffrn_refln must uniquely identify the reflection in the data set identified by the item attribute diffrn_id. in category diffrn_refln Note that this item need not be a number; it can be any unique identifier. Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set. The residual [sum|avdel(I)| / sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The avdel(I) term is the average absolute difference between av(I) and the individual symmetry-equivalent intensities. Measure [sum|sigma(I)|/sum|net(I)|] for all measured reflections. Measure [sum u(net I)|/sum|net I|] for all measured reflections. The maximum value of the Miller index h for the reflection data specified by attribute index_h in category diffrn_refln. The minimum value of the Miller index h for the reflection data specified by attribute index_h in category diffrn_refln. The maximum value of the Miller index k for the reflection data specified by attribute index_k in category diffrn_refln. The minimum value of the Miller index k for the reflection data specified by attribute index_k in category diffrn_refln. The maximum value of the Miller index l for the reflection data specified by attribute index_l in category diffrn_refln. The minimum value of the Miller index l for the reflection data specified by attribute index_l in category diffrn_refln. The total number of measured intensities, excluding reflections that are classified as systematically absent. The R factor for merging the reflections that satisfy the resolution limits established by attribute d_resolution_high in category diffrn_reflns and attribute d_resolution_low in category diffrn_reflns and the observation limit established by attribute observed_criterion. in category diffrn_reflns Rmerge(I) = [sum~i~(sum~j~|I~j~ - |)] / [sum~i~(sum~j~)] I~j~ = the intensity of the jth observation of reflection i = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The R factor for averaging the symmetry related reflections to a unique data set. Overall Chi-squared statistic for the data set. The highest resolution for the interplanar spacings in the reflection data set. This is the smallest d value. The lowest resolution for the interplanar spacings in the reflection data set. This is the largest d value. The number of reflections satisfying the observation criterion as in attribute pdbx_observed_criterion in category diffrn_reflns The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _diffrn_reflns.d_resolution_high and _diffrn_reflns.d_resolution_low and the observation limit established by attribute observed_criterion. in category diffrn_reflns The overall redundancy for the data set. The number of rejected reflections in the data set. The reflections may be rejected by setting the observation criterion, attribute observed_criterion in category diffrn_reflns. A description of the process used to reduce the intensity data into structure-factor magnitudes. data averaged using Fisher test Maximum theta angle in degrees for the measured diffraction intensities. Minimum theta angle in degrees for the measured diffraction intensities. The [1][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [1][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [1][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [2][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [2][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [2][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [3][1] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [3][2] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. The [3][3] element of the 3x3 matrix used to transform Miller indices in the DIFFRN_REFLN category into the Miller indices in the REFLN category. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment. Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. Each reflection class is defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. <PDBx:diffrn_reflns_classCategory> <PDBx:diffrn_reflns_class code="Main"> <PDBx:av_R_eq>0.015</PDBx:av_R_eq> <PDBx:d_res_high>0.551</PDBx:d_res_high> <PDBx:d_res_low>6.136</PDBx:d_res_low> <PDBx:description>m=0; main reflections</PDBx:description> <PDBx:number>1580</PDBx:number> </PDBx:diffrn_reflns_class> <PDBx:diffrn_reflns_class code="Sat1"> <PDBx:av_R_eq>0.010</PDBx:av_R_eq> <PDBx:d_res_high>0.551</PDBx:d_res_high> <PDBx:d_res_low>6.136</PDBx:d_res_low> <PDBx:description>m=1; first-order satellites</PDBx:description> <PDBx:number>1045</PDBx:number> </PDBx:diffrn_reflns_class> </PDBx:diffrn_reflns_classCategory> For each reflection class, the residual [sum av|del(I)|/sum|av(I)|] for symmetry-equivalent reflections used to calculate the average intensity av(I). The av|del(I)| term is the average absolute difference between av(I) and the individual intensities. Measure [sum|sigma(net I)|/sum|net I|] for all measured intensities in a reflection class. Measure [sum|u(net I)|/sum|net I|] for all measured intensities in a reflection class. The smallest value in angstroms for the interplanar spacings for the reflections in each measured reflection class. This is called the highest resolution for this reflection class. The largest value in angstroms of the interplanar spacings for the reflections for each measured reflection class. This is called the lowest resolution for this reflection class. Description of each reflection class. m=1 first order satellites H0L0 common projection reflections The total number of measured intensities for each reflection class, excluding the systematic absences arising from centring translations. The code identifying a certain reflection class. 1 m1 s2 Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set. Example 1 - based on CAD-4 diffractometer data obtained for Yb(S-C5H4N)2(THF)4. <PDBx:diffrn_scale_groupCategory> <PDBx:diffrn_scale_group code="A24"> <PDBx:I_net>1.021</PDBx:I_net> </PDBx:diffrn_scale_group> </PDBx:diffrn_scale_groupCategory> The scale for a specific measurement group which is to be multiplied with the net intensity to place all intensities in the DIFFRN_REFLN or REFLN list on a common scale. The value of attribute code in category diffrn_scale_group must uniquely identify a record in the DIFFRN_SCALE_GROUP list. Note that this item need not be a number; it can be any unique identifier. 1 2 c1 c2 Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:diffrn_sourceCategory> <PDBx:diffrn_source diffrn_id="s1"> <PDBx:current>180</PDBx:current> <PDBx:power>50</PDBx:power> <PDBx:size>8mm x 0.4 mm broad-focus</PDBx:size> <PDBx:source>rotating anode</PDBx:source> <PDBx:type>Rigaku RU-200</PDBx:type> </PDBx:diffrn_source> </PDBx:diffrn_sourceCategory> The current in milliamperes at which the radiation source was operated. A description of special aspects of the radiation source used. Beamline for synchrotron source. 6A2 7.2 9.5 9.6 A-1 A1 BL-6A BW6 BW7B F-1 F1 PX7.2 PX9.6 UNDULATOR W32 WIGGLER X11 X12C X25 X26-C X31 X4A X8C Synchrotron beamline. Synchrotron site. Yes/No if synchrotron source was used or not. Y N Wavelength of radiation. Comma separated list of wavelengths or wavelength range. The power in kilowatts at which the radiation source was operated. The dimensions of the source as viewed from the sample. 8mm x 0.4 mm fine-focus broad focus The general class of the radiation source. sealed X-ray tube nuclear reactor spallation source electron microscope rotating-anode X-ray tube synchrotron The complement of the angle in degrees between the normal to the surface of the X-ray tube target and the primary X-ray beam for beams generated by traditional X-ray tubes. 1.5 The chemical element symbol for the X-ray target (usually the anode) used to generate X-rays. This can also be used for spallation sources. The make, model or name of the source of radiation. NSLS beamline X8C Rigaku RU200 The voltage in kilovolts at which the radiation source was operated. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections. Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_standard_reflnCategory> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>3</PDBx:index_h> <PDBx:index_k>2</PDBx:index_k> <PDBx:index_l>4</PDBx:index_l> </PDBx:diffrn_standard_refln> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>1</PDBx:index_h> <PDBx:index_k>9</PDBx:index_k> <PDBx:index_l>1</PDBx:index_l> </PDBx:diffrn_standard_refln> <PDBx:diffrn_standard_refln code="1" diffrn_id="s1"> <PDBx:index_h>3</PDBx:index_h> <PDBx:index_k>0</PDBx:index_k> <PDBx:index_l>10</PDBx:index_l> </PDBx:diffrn_standard_refln> </PDBx:diffrn_standard_reflnCategory> Miller index h of a standard reflection used in the diffraction measurement process. Miller index k of a standard reflection used in the diffraction measurement process. Miller index l of a standard reflection used in the diffraction measurement process. The code identifying a reflection measured as a standard reflection with the indices attribute index_h, in category diffrn_standard_refln attribute index_k in category diffrn_standard_refln and attribute index_l in category diffrn_standard_refln. This is the same code as the attribute standard_code in category diffrn_refln in the DIFFRN_REFLN list. 1 2 c1 c2 This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:diffrn_standardsCategory> <PDBx:diffrn_standards diffrn_id="s1"> <PDBx:decay_>0</PDBx:decay_> <PDBx:interval_time>120</PDBx:interval_time> <PDBx:number>3</PDBx:number> </PDBx:diffrn_standards> </PDBx:diffrn_standardsCategory> The percentage decrease in the mean of the intensities for the set of standard reflections from the start of the measurement process to the end. This value usually affords a measure of the overall decay in crystal quality during the diffraction measurement process. Negative values are used in exceptional instances where the final intensities are greater than the initial ones. The number of reflection intensities between the measurement of standard reflection intensities. The time in minutes between the measurement of standard reflection intensities. The number of unique standard reflections used during the measurement of the diffraction intensities. The standard uncertainty (estimated standard deviation) of the individual mean standard scales applied to the intensity data. The standard uncertainty of the individual mean standard scales applied to the intensity data. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. Data items in the EM_SYMMETRY_2DX category record 2D crystal symmetry parameters utilized in a 3DEM reconstruction. Unit-cell angle gamma in degrees. Length used to sample the reciprocal lattice lines in the c-direction. Corresponding key in _em_entity_assembly category. Unit-cell length a in Angstroms. Unit-cell length b in Angstroms. Thickness of 2D crystal There are 17 plane groups classified as oblique, rectangular, square, and hexagonal. To describe the symmetry of 2D crystals of biological molecules, plane groups are expanded to equivalent noncentrosymmetric space groups. The 2D crystal plane corresponds to the 'ab' plane of the space group. Enumerated space group descriptions include the plane group number in parentheses, the H-M plane group symbol, and the plane group class. Unique key for the 2d_crystal_entity category. pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category. Data items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. Example 1 <PDBx:em_2d_projection_selectionCategory> <PDBx:em_2d_projection_selection entry_id="1ABC"> <PDBx:details xsi:nil="true" /> <PDBx:method>INTERACTIVE</PDBx:method> <PDBx:num_particles>52346</PDBx:num_particles> <PDBx:software_name>EMAN2 BOXER</PDBx:software_name> </PDBx:em_2d_projection_selection> </PDBx:em_2d_projection_selectionCategory> This data item is a pointer to attribute id in category citation in the CITATION category. Any additional details used for selecting observed assemblies. negative monitor contrast facilitated particle picking unique identifier for each projection selection description The method used for selecting observed assemblies. particles picked interactively from monitor The number of particles selected from the projection set of images. 840 The software used to select 2d projections. entry id Data items in the EM_SYMMETRY_3DX category record 3D crystal symmetry parameters utilized in 3DEM reconstruction averaging. Unit-cell angle alpha in degrees. Unit-cell angle beta in degrees. Unit-cell angle gamma in degrees. Unit-cell length a in Angstroms. Unit-cell length b in Angstroms. Unit-cell length c in Angstroms. Space group name. P 1 P 21 21 2 I 4 H 3 Space group number. Unique key for the em_3d_crystal_entity category. pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category. Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_fittingCategory> <PDBx:em_3d_fitting entry_id="1DYL" id="1"> <PDBx:details> THE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM CHOI ET AL (1997) PROTEINS 3 27:345-359 (SUBUNIT A OF PDB FILE 1VCQ) WAS PLACED INTO THE CRYO-EM DENSITY MAP. THE CAPSID PROTEIN WAS FIRST MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO POSITIONS OF THE FOUR INDEPENDENT MONOMER DENSITIES BETWEEN THE INNER LEAFLET OF THE BILAYER AND THE RNA. THESE POSITIONS WERE THEN REFINED BY RIGID BODY REFINEMENT IN REAL SPACE WITH THE PROGRAM EMFIT (CHENG ET AL. 1995, CELL 80, 621-630). THE QUALITY OF THE FIT CAN BE SEEN FROM THE MAP DENSITY WITHIN THE PROTEIN. ALL 4563 ATOMS ARE IN DENSITY OF AT LEAST 4 SIGMA (96.73) ABOVE THE AVERAGE (512.04), 1167 ATOMS ARE IN DENSITY BETWEEN 4 AND 5 SIGMA, 3174 ATOMS ARE IN DENSITY BETWEEN 5 AND 6 SIGMA, AND 222 ATOMS ARE IN DENSTY OF 6 SIGMA OR ABOVE. THE VARIATION IN DENSITY OVER THE FITTED PROTEIN CAN BE VISUALIZED WITH THE PSEUDO TEMPERATURE FACTOR. THE DENSITY VALUE AT EACH ATOM IS GIVEN IN THE 8TH COLUM (USUALLY THE OCCUPANCY) AS THE NUMBER OF STANDARD DEVIATION ABOVE BACKGROUND. COLUMN NINE (USUALLY THE TEMPERATURE FACTOR) CONTAINS THE VALUE OF THE RELATIVE DENSITY WITHIN THE FITTED PROTEIN SCALED LINEARLY SO THAT THE MINIMUM DENSITY IS 100.0 AND THE MAXIMUM DENSITY IS 1.0. THE ATOMS THAT LIE IN THE LOWER DENSITY REGIONS WILL HAVE THE HIGHEST PSEUDO TEMPERATURE FACTORS.</PDBx:details> <PDBx:method>AUTOMATIC</PDBx:method> <PDBx:overall_b_value xsi:nil="true" /> <PDBx:ref_protocol>RIGID BODY REFINEMENT</PDBx:ref_protocol> <PDBx:ref_space>REAL</PDBx:ref_space> <PDBx:software_name>1</PDBx:software_name> <PDBx:target_criteria>R-FACTOR</PDBx:target_criteria> </PDBx:em_3d_fitting> </PDBx:em_3d_fittingCategory> Any additional details regarding fitting of atomic coordinates into the 3DEM volume, including data and considerations from other methods used in computation of the model. Initial local fitting was done using Chimera and then NMFF was used for flexible fitting. The method used to fit atomic coordinates into the 3dem reconstructed map. The overall B (temperature factor) value for the 3d-em volume. 200 The refinement protocol used. Local refinement, Flexible fitting A flag to indicate whether fitting was carried out in real or reciprocal refinement space. The software used for fitting atomic coordinates to the map. Situs, NMFF, YUP.scx, etc. The measure used to assess quality of fit of the atomic coordinates in the 3DEM map volume. Cross-correlation coefficient This data item is a pointer to _entry_id in the ENTRY category. The value of attribute id in category em_3d_fitting must uniquely identify a fitting procedure of atomic coordinates into 3dem reconstructed map volume. Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_fitting_listCategory> <PDBx:em_3d_fitting_list _3d_fitting_id="l" id="1"> <PDBx:pdb_chain_id xsi:nil="true" /> <PDBx:pdb_entry_id>1VCQ</PDBx:pdb_entry_id> </PDBx:em_3d_fitting_list> </PDBx:em_3d_fitting_listCategory> Details about the model used in fitting. The ID of the biopolymer chain used for fitting, e.g., A. Please note that only one chain can be specified per instance. If all chains of a particular structure have been used for fitting, this field can be left blank. The molecular entities represented in this fitting description. The PDB code for the entry used in fitting. PDB entry 1EHZ The value of attribute 3d_fitting_id in category em_3d_fitting_list is a pointer to attribute id in category em_3d_fitting in the 3d_fitting category This data item is a unique identifier. Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_3d_reconstructionCategory> <PDBx:em_3d_reconstruction id="1"> <PDBx:actual_pixel_size>2.52</PDBx:actual_pixel_size> <PDBx:ctf_correction_method xsi:nil="true" /> <PDBx:details xsi:nil="true" /> <PDBx:entry_id>1DYL</PDBx:entry_id> <PDBx:method>CROSS-COMMON LINES</PDBx:method> <PDBx:nominal_pixel_size>2.64</PDBx:nominal_pixel_size> <PDBx:resolution>9</PDBx:resolution> <PDBx:resolution_method xsi:nil="true" /> </PDBx:em_3d_reconstruction> </PDBx:em_3d_reconstructionCategory> The actual pixel size of projection set of images. 2.8 5.76 The algorithm used project from 2D orientations to 3D map. This data item is a pointer to attribute id in category citation in the CITATION category. The CTF-correction method. The Contrast Transfer Function CTF compensation for low contrast specimens (e.g. frozen-hydrated), for which phase contrast is the only significant mechanism, then higher defocus levels must be used to achieve any significant transfer, and several images at different focus levels must be combined to complete the information lost from the transfer gaps of any one image. The CTF correction can be applied to each extracted particle separately or to the whole micrograph after digitisation. The simplest level of compensation is to reverse phases at the negative lobes of the CTF. The volumes were CTF-corrected in defocus groups, with an average of approximately 999 individual images per group Any additional details used in the 3d reconstruction. a modified version of SPIDER program was used for the reconstruction This data item is a pointer to attribute id in category entry in the ENTRY category. euler angles details type of FSC curve used to determine map resolution Gold standard The magnification calibration method for the 3d reconstruction. TMV images The algorithm method used for the 3d-reconstruction. cross-common lines polar Fourier transform (PFT) The nominal pixel size of the projection set of images. 3.11 6.78 This item was correspondence to two type of em dataset processing_emDataSet_singleParticle.numClassAverages processing_emDataSet_icosahedral.numClassAverages The number of 2D projections or 3D subtomograms used in the 3d reconstruction type of refinement performed in order to determine map resolution HALF-MAPS REFINED INDEPENDENTLY The final resolution (in Angstroms)of the 3D reconstruction. 8.9 10.0 The method used to determine the final resolution of the 3d reconstruction. The Fourier Shell Correlation criterion as a measure of resolution is based on the concept of splitting the (2D) data set into two halves; averaging each and comparing them using the Fourier Ring Correlation (FRC) technique. FSC at 0.5 cut-off software name The type of symmetry applied to the reconstruction The value of attribute id in category em_3d_reconstruction must uniquely identify the 3d reconstruction. Foreign key to the EM_IMAGE_PROCESSING category Administration-related data items Example 1 <PDBx:em_adminCategory> <PDBx:em_admin entry_id="D_100005"> <PDBx:current_status>REL</PDBx:current_status> <PDBx:deposition_date>2008-12-01</PDBx:deposition_date> <PDBx:details xsi:nil="true" /> <PDBx:last_update>2011-05-22</PDBx:last_update> <PDBx:map_release_date>2009-12-01</PDBx:map_release_date> </PDBx:em_admin> </PDBx:em_adminCategory> This data item indicates the current status of the EMDB entry. date of the entry deposition entry deposition site EMDB administration details date of header information release for this entry date of last update to the file date of the embargo expiration for this map entry date of map release for this entry date that map entry was obsoleted This item indicates that the current entry replaced a previously released structure. Title for the EMDB entry. This data item is a pointer to attribute id in category entry. Data items in the EM_ASSEMBLY category record details about the imaged EM sample. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_assemblyCategory> <PDBx:em_assembly entry_id="1DYL" id="1"> <PDBx:aggregation_state>PARTICLE</PDBx:aggregation_state> <PDBx:composition>virus</PDBx:composition> <PDBx:details xsi:nil="true" /> <PDBx:mol_wt_exp xsi:nil="true" /> <PDBx:mol_wt_method xsi:nil="true" /> <PDBx:mol_wt_theo xsi:nil="true" /> <PDBx:name>virus</PDBx:name> <PDBx:num_components>1</PDBx:num_components> </PDBx:em_assembly> </PDBx:em_assemblyCategory> A description of the aggregation state of the assembly. The composition of the assembly. Protein/DNA complex Virus Any additional details describing the imaged sample. The sample was monodisperse The value (in megadaltons) of the experimentally determined molecular weight of the assembly. 3.5 The method used to determine the molecular weight. The value (in megadaltons) of the theoretically determined molecular weight of the assembly. 3.5 The name of the assembly of observed complexes. MaB1 Fab Fragment bound to Human Rhinovirus The number of components of the biological assembly. 3 This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_assembly must uniquely identify a collection of observed complexes. Category to collect the authors of this entry Example 1 <PDBx:em_author_listCategory> <PDBx:em_author_list ordinal="1"> <PDBx:author>Miller, A.</PDBx:author> </PDBx:em_author_list> <PDBx:em_author_list ordinal="2"> <PDBx:author>Smith, J.T.</PDBx:author> </PDBx:em_author_list> </PDBx:em_author_listCategory> Author of the EMDB entry in PDB format: Taylor, T.J. Taylor, D.J. The Open Researcher and Contributor ID (ORCID). 0000-0002-6681-547X ID 1 corresponds to the main author of the entry Data items in the BUFFER category record details of the sample buffer. Additional details about the buffer. 20mM NaCl, 10mM Tris-HCL,1mM MgCl2,1mM EDTA The name of the buffer. Polymix buffer The pH of the sample buffer. The value of attribute id in category em_buffer must uniquely identify the sample buffer. pointer to attribute id in category em_specimen Buffer category The concentration of the sample (arbitrary units). 1.35 Units for the sample concentration value. mg/mL formula for buffer component NaCl name of the buffer component sodium chloride Foreign key to the entry category. This data item is the primary key of the category. Description of growth of a 2D, 3D, or helical crystal array. The type of atmosphere in which crystals were grown Crystallization was performed in an environmental chamber with constant nitrogen gas flow. Description of growth of a 2D, 3D, or helical crystal array. Lysozyme (200 mg/ml) was mixed 1 to 1 with precipitant solution (3.5M sodium chloride, 15% PEG5000, 50 mM sodium acetate pH 4.5). Microcrystals were grown by the hanging drop method. Instrument used to prepare the crystalline array Langmuir trough Gryphon LCP Description of the lipid mixture used for crystallization monoolein and monopalmitolein were mixed 1:1 The molar ratio of lipid to protein in the crystallized sample 5.0 Foreign key relationship to the EMD SPECIMEN category The value of the temperature in degrees Kelvin used for growing the crystals. 298 Time period for array crystallization, in time unit indicated (min, hr, day, month, year) 50 Time unit for array crystallization This data item is the primary key of the category. Description of the Contrast Transfer Function (CTF) correction Example 1 <PDBx:em_ctf_correctionCategory> <PDBx:em_ctf_correction id="1"> <PDBx:em_image_processing_id>1</PDBx:em_image_processing_id> <PDBx:type>PHASE FLIPPING ONLY</PDBx:type> </PDBx:em_ctf_correction> </PDBx:em_ctf_correctionCategory> Yes if CTF amplitude correction was performed Amplitude correction factor used in CTF correction CTF amplitude correction space CTF correction operation Any additional details about CTF correction CTF amplitude correction was performed following 3D reconstruction Foreign key to the EM_IMAGE_PROCESSING category Yes if Phase reversal (flipping) was performed Yes if Anisotropic phase reversal (flipping) was performed CTF phase reversal correction space Type of CTF correction applied Primary key Category holds links to raw data sources for the entry, e.g., held by a remote server. Example 1 <PDBx:em_db_referenceCategory> <PDBx:em_db_reference id="1"> <PDBx:access_code>1ABC</PDBx:access_code> <PDBx:db_name>PDB</PDBx:db_name> </PDBx:em_db_reference> </PDBx:em_db_referenceCategory> Unique identifier for a provided link. 1ABC EMD-5002 The name of the database containing the related entry. A description of the related entry. map derived from same data with D7 symmetry imposed model derived from X-ray crystal structure 1ABC Indicates relationship of this entry with other entries in PDB and EMDB. The name of the database containing the related entry. Category holds links to raw data sources for the entry, e.g., held by a remote server. Example 1 <PDBx:em_db_reference_auxiliaryCategory> <PDBx:em_db_reference_auxiliary id="1"> <PDBx:link>http://www.ebi.ac.uk/pdbe/emdb/singleParticledir/SPIDER_FRANK_data</PDBx:link> <PDBx:link_type>2D EM DATA</PDBx:link_type> </PDBx:em_db_reference_auxiliary> </PDBx:em_db_reference_auxiliaryCategory> Hyperlink to the auxiliary data. Type of auxiliary data stored at the indicated link. Unique identifier for a provided link. Data items in the EM_DEPOSITOR INFO category record parameters for EM depositions that are provided by the depositor Example 1 <PDBx:em_depositor_infoCategory> <PDBx:em_depositor_info entry_id="D_10005049"> <PDBx:em_method_selection>yes</PDBx:em_method_selection> <PDBx:molecular_description_flag>yes</PDBx:molecular_description_flag> </PDBx:em_depositor_info> </PDBx:em_depositor_infoCategory> The selected EM experimental method. Records whether molecular/polymer entities of the EM sample will be described. This data item is a pointer to the ENTRY category. Some internal items to power the deposition interface Example 1 <PDBx:em_depuiCategory> <PDBx:em_depui entry_id="1ABC"> <PDBx:depositor_hold_instructions>HOLD</PDBx:depositor_hold_instructions> <PDBx:macromolecule_description>YES</PDBx:macromolecule_description> <PDBx:obsolete_instructions xsi:nil="true" /> <PDBx:same_authors_as_pdb>NO</PDBx:same_authors_as_pdb> <PDBx:same_title_as_pdb>NO</PDBx:same_title_as_pdb> </PDBx:em_depui> </PDBx:em_depuiCategory> Choose the manner in which you would like the map and associated files (half maps, additional maps, masks, FSC curves, structure factors, layer lines, and images) to be released. Release of these files can be delayed either until publication of the associated primary citation or until one year after completion of the deposition. It is the responsibility of the depositor to notify the EMDB when the primary citation has been published. Please note that map-associated experimental information and metadata (header data) are made available to the public when an entry is placed on hold. Indicates whether the authors are providing a macromolecule level description of their sample Instruction for annotators on why a previous released entry should be obsoleted. Example of valid request: * Author wants to replace a map that has already been released, following discovery of a processing error Examples of invalid requests: * Someone other than the author wants to obsolete a map. * Legal conflict of interest Obsoletion is not required for the following actions: * to change released metadata info. * to update the map of an HPUB entry. * to change the hand of a released map. * to deposit an improved version of a released map. Indicates whether the authors for the EMDB entry are the same as for the PDB entry in a joint map + model deposition Indicates whether the title for the EMDB entry is the same as for the PDB entry in a joint map + model deposition Primary key Data items in the EM_DETECTOR category record details of the image detector type. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_detectorCategory> <PDBx:em_detector entry_id="1DYL" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:detective_quantum_efficiency xsi:nil="true" /> <PDBx:type>KODAK SO163 FILM</PDBx:type> </PDBx:em_detector> </PDBx:em_detectorCategory> Any additional information about the detection system. Any other details regarding the detector. The detective_quantum_efficiency (DQE)is defined as the square of the signal-to-noise ratio in the recording device divided by the square of the signal-to-ratio in the electron beam: (SIGNAL/NOISE)2 recording device DQE = ------------------------------- (SIGNAL/NOISE)2 electron beam A DQE value of 1 indicates a perfect recorder. "DQE = 0.25" menas that the signal-to-noise ratio is reduced by half in the recording step. (0.5)**2 DQE = --------- = 0.25. (1.0)**2 0.25 The detector mode used during image recording. The detector type used for recording images. Usually film or CCD camera. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_detector must uniquely identify the detector used for imaging. Microscopy parameters relevant only for crystallography Example 1 <PDBx:em_diffractionCategory> <PDBx:em_diffraction id="1"> <PDBx:camera_length>800</PDBx:camera_length> <PDBx:imaging_id>1</PDBx:imaging_id> </PDBx:em_diffraction> <PDBx:em_diffraction id="2"> <PDBx:camera_length>750</PDBx:camera_length> <PDBx:imaging_id>2</PDBx:imaging_id> </PDBx:em_diffraction> </PDBx:em_diffractionCategory> TODO 800 Foreign key to the EM_IMAGING category Comma-separated list of tilt angles (in degrees) used in the electron diffraction experiment. 20,40,50,55 Primary key Statistical parameters for electron diffraction measurements within a resolution shell Example 1 <PDBx:em_diffraction_shellCategory> <PDBx:em_diffraction_shell id="1"> <PDBx:fourier_space_coverage>93.0</PDBx:fourier_space_coverage> <PDBx:high_resolution>7.5</PDBx:high_resolution> <PDBx:low_resolution>45</PDBx:low_resolution> <PDBx:multiplicity>2.3</PDBx:multiplicity> <PDBx:num_structure_factors>327</PDBx:num_structure_factors> <PDBx:phase_residual>13.5</PDBx:phase_residual> </PDBx:em_diffraction_shell> </PDBx:em_diffraction_shellCategory> Pointer to EM CRYSTALLOGRAPHY STATS Completeness of the structure factor data within this resolution shell, in percent 93.2 High resolution limit for this shell (Angstroms) 3.0 Low resolution limit for this shell (Angstroms) 5.5 Multiplicity (average number of measurements) for the structure factors in this resolution shell 2.5 Number of measured structure factors in this resolution shell 244 Phase residual for this resolution shell, in degrees 13.5 Unique identifier for the category em_diffraction_shell Statistical parameters for electron diffraction measurements Example 1 <PDBx:em_diffraction_statsCategory> <PDBx:em_diffraction_stats id="1"> <PDBx:fourier_space_coverage>92</PDBx:fourier_space_coverage> <PDBx:high_resolution>7.2</PDBx:high_resolution> <PDBx:num_intensities_measured>1524</PDBx:num_intensities_measured> <PDBx:num_structure_factors>325</PDBx:num_structure_factors> <PDBx:overall_phase_error>18.6</PDBx:overall_phase_error> <PDBx:overall_phase_residual>9.5</PDBx:overall_phase_residual> <PDBx:phase_error_rejection_criteria>None</PDBx:phase_error_rejection_criteria> <PDBx:r_merge>19.5</PDBx:r_merge> <PDBx:r_sym>23.2</PDBx:r_sym> </PDBx:em_diffraction_stats> </PDBx:em_diffraction_statsCategory> Any addition details about the structure factor measurements Phases were obtained from micrograph images of the 2D crystals Completeness of the structure factor data within the defined space group at the reported resolution (percent). 89.3 High resolution limit of the structure factor data, in Angstroms 7.5 Pointer to attribute id in category em_image_processing Total number of diffraction intensities measured (before averaging) 1590 Number of structure factors obtained (merged amplitudes + phases) 325 Overall phase error in degrees 17.5 Overall phase residual in degrees 17.5 Criteria used to reject phases Structure factors with phase errors higher than 20 degrees were omitted from refinement Rmerge value (percent) 19.8 Rsym value (percent) 24.4 Identifier for this category Sugar embedding category Staining procedure used in the specimen preparation. The crystal suspension was injected into the lens of a drop of buffer containing 1 % tannin sitting on a carbon film supported by a molybdenum grid. An equal volume of 1% glucose was then added and the solution thoroughly but gently mixed. The grid was then blotted, air dried, and frozen in LN2. The embedding material. tannin and glucose Foreign key relationship to the EMD SPECIMEN category This data item is the primary key of the category. Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex. Example 1 -- based on PDB entry 1C2W <PDBx:em_entity_assemblyCategory> <PDBx:em_entity_assembly id="1"> <PDBx:name>50S Ribosomal Subunit</PDBx:name> <PDBx:parent_id>0</PDBx:parent_id> <PDBx:type>RIBOSOME</PDBx:type> </PDBx:em_entity_assembly> </PDBx:em_entity_assemblyCategory> Example 2 -- based on PDB entry 3IY7 <PDBx:em_entity_assemblyCategory> <PDBx:em_entity_assembly id="1"> <PDBx:name>Fab fragment from MAb F interacting with feline panleukopenia virus (FPV)</PDBx:name> <PDBx:parent_id>0</PDBx:parent_id> <PDBx:type>COMPLEX</PDBx:type> </PDBx:em_entity_assembly> <PDBx:em_entity_assembly id="2"> <PDBx:name>feline panleukopenia virus</PDBx:name> <PDBx:parent_id>1</PDBx:parent_id> <PDBx:synonym>FPV</PDBx:synonym> <PDBx:type>VIRUS</PDBx:type> </PDBx:em_entity_assembly> <PDBx:em_entity_assembly id="3"> <PDBx:name>Fab fragment from Mab F</PDBx:name> <PDBx:parent_id>1</PDBx:parent_id> <PDBx:synonym>Fab</PDBx:synonym> <PDBx:type>COMPLEX</PDBx:type> </PDBx:em_entity_assembly> </PDBx:em_entity_assemblyCategory> This data item is a pointer to attribute id in category em_assembly in the ASSEMBLY category. An indication if an assembly is contains a chimeric polymer Additional details about the component. Fab fragment generated by proteolytic cleavage of LA2 IgG antibody. The cell from which the component was obtained. CHO HELA 3T3 The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane A flag to indicate whether the component is engineered. The expression system used to produce the component. eschericia coli saccharomyces cerevisiae The plasmid used to produce the component. pBR322 pMB9 The organelle from which the component was obtained. golgi mitochondrion cytoskeleton The common name of the species of the natural organism from which the component was obtained. The species of the natural organism from which the component was obtained. The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 The tissue of the natural organism from which the component was obtained. heart liver eye lens macromolecules associated with this component, if defined as comma separated list of entity ids (integers). The Gene Ontology (GO) identifier for the component. The GO id is the appropriate identifier used by the Gene Ontology Consortium. Reference: Nature Genetics vol 25:25-29 (2000). GO:0005876 GO:0015630 The InterPro (IPR) identifier for the component. The IPR id is the appropriate identifier used by the Interpro Resource. Reference: Nucleic Acid Research vol 29(1):37-40(2001). 001304 002353 mutant flag Name of this component in the observed assembly. Ternary complex of alpha-tubulin with tubulin folding cofactors TBCE and TBCB 80S Ribosome bound to emetine messenger RNA initiation factor 2 GroEL antibody Fab fragment number of copies oligomeric details The parent of this assembly. This data item is an internal category pointer to attribute id. in category em_entity_assembly By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero). The assembly type. Alternative name of the component. FADV-1 A description of types of components of the assembly of the biological structure. The value of attribute id in category em_entity_assembly identifies one component of the complex. Data items in this category record details about the molecular weight of an assembly component of the sample. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_entity_assembly_molwtCategory> <PDBx:em_entity_assembly_molwt entity_assembly_id="1" id="1"> <PDBx:units>MEGADALTONS</PDBx:units> <PDBx:value>30.5</PDBx:value> </PDBx:em_entity_assembly_molwt> </PDBx:em_entity_assembly_molwtCategory> Identifies whether the given molecular weight was derived experimentally. The method used to determine the molecular weight. Molecular weight units. The molecular weight of the assembly component. 0.53 A reference to attribute id in category em_entity_assembly which uniquely identifies one assembly or assembly component of the imaged sample. Ordinal key for the em_entity_assembly_molwt category. Data items in this category record taxonomic details about the natural source for EM assemblies and assembly components. Example 1 <PDBx:em_entity_assembly_naturalsourceCategory> <PDBx:em_entity_assembly_naturalsource entity_assembly_id="8333" id="1"> <PDBx:cellular_location xsi:nil="true" /> <PDBx:ncbi_tax_id>Escherichia coli</PDBx:ncbi_tax_id> <PDBx:organ xsi:nil="true" /> <PDBx:organelle>cytoplasm</PDBx:organelle> <PDBx:organism>K12</PDBx:organism> <PDBx:strain xsi:nil="true" /> <PDBx:tissue xsi:nil="true" /> </PDBx:em_entity_assembly_naturalsource> </PDBx:em_entity_assembly_naturalsourceCategory> The cell type from which the component was obtained. CHO HELA 3T3 The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane The NCBI taxonomy id for the natural organism source of the component. 10804 9606 The organ of the organism from which the component was obtained. Escherichia coli The organelle from which the component was obtained. Golgi Mitochondrion Cytoskeleton The genus-species of the natural organism from which the component was obtained. Escherichia coli The strain of the natural organism from which the component was obtained, if relevant. DH5a BMH 71-18 The tissue of the natural organism from which the component was obtained. Cartilage Liver Eye lens Pointer to the assembly component defined in the EM ENTITY ASSEMBLY category. Ordinal key for the em_entity_assembly_naturalsource category. Data items in this category record details about recombinant expression of the assembly or assembly component. Example 1 <PDBx:em_entity_assembly_recombinantCategory> <PDBx:em_entity_assembly_recombinant entity_assembly_id="1" id="1"> <PDBx:organism>Escherichia coli</PDBx:organism> <PDBx:plasmid>pET17c</PDBx:plasmid> </PDBx:em_entity_assembly_recombinant> </PDBx:em_entity_assembly_recombinantCategory> The cell of the host organism from which the expressed component was obtained, if relevant. Potato root The NCBI taxonomy id of the expression host used to produce the component. Expression system host organism used to produce the component. escherichia coli saccharomyces cerevisiae The plasmid used to produce the component in the expression system. pBR322 pMB9 The strain of the host organism from which the expresed component was obtained, if relevant. DH5a BMH 71-18 Pointer to the expressed component described in the EM ENTITY ASSEMBLY category. Ordinal identifier Data items in this category record taxonomic details about the synthetic source for EM assemblies and assembly components. Example 1 <PDBx:em_entity_assembly_syntheticCategory> <PDBx:em_entity_assembly_synthetic entity_assembly_id="1" id="1"> <PDBx:cellular_location xsi:nil="true" /> <PDBx:ncbi_tax_id>8333</PDBx:ncbi_tax_id> <PDBx:organ xsi:nil="true" /> <PDBx:organelle xsi:nil="true" /> <PDBx:organism>Escherichia coli</PDBx:organism> <PDBx:strain>K12</PDBx:strain> <PDBx:tissue xsi:nil="true" /> </PDBx:em_entity_assembly_synthetic> </PDBx:em_entity_assembly_syntheticCategory> The cell type from which the component was obtained. CHO HELA 3T3 The cellular location of the component. cytoplasm endoplasmic reticulum plasma membrane The NCBI taxonomy id for the synthetic organism source of the component. 10804 9606 The organ of the organism from which the component was obtained. Escherichia coli The organelle from which the component was obtained. Golgi Mitochondrion Cytoskeleton The genus-species of the synthetic organism from which the component was obtained. Escherichia coli The strain of the synthetic organism from which the component was obtained, if relevant. DH5a BMH 71-18 The tissue of the synthetic organism from which the component was obtained. Cartilage Liver Eye lens Pointer to the assembly component defined in the EM ENTITY ASSEMBLY category. Ordinal key for the em_entity_assembly_synthetic category. Category to describe the euler angle assignement Example 1 <PDBx:em_euler_angle_assignmentCategory> <PDBx:em_euler_angle_assignment id="1"> <PDBx:image_processing_id>1</PDBx:image_processing_id> <PDBx:order>FINAL</PDBx:order> <PDBx:type>COMMON LINE</PDBx:type> </PDBx:em_euler_angle_assignment> </PDBx:em_euler_angle_assignmentCategory> Any additional details about euler angle assignment Foreign key to the EM_IMAGE_PROCESSING category Stage of the reconstruction in which the angle assignments were made. Angular sampling of projection matching 1.5 Overall figure of merit for projection matching Number of reference projections used for euler angle assignment The procedure used to assigned euler angles. Primary key Data items in the EM_EXPERIMENT category provide high-level classification of the EM experiment. Example 1 - based on PDB entry 1EG0 <PDBx:em_experimentCategory> <PDBx:em_experiment entry_id="1EG0"> <PDBx:aggregation_state>PARTICLE</PDBx:aggregation_state> <PDBx:reconstruction_method>SINGLE PARTICLE</PDBx:reconstruction_method> <PDBx:specimen_type>VITREOUS ICE (CRYO EM)</PDBx:specimen_type> </PDBx:em_experiment> </PDBx:em_experimentCategory> The aggregation/assembly state of the imaged specimen. Foreign key to the EM_ENTITY_ASSEMBLY category Placeholder ID. The reconstruction method used in the EM experiment. The specimen type used in the EM experiment. VITREOUS ICE (CRYO EM) NEGATIVE STAIN FREEZE SUBSTITUTION This data item is a pointer to attribute id in category entry in the ENTRY category. Description of fiducial markers. Diameter of the fiducial markers 14 Foreign key relationship to the EMD SPECIMEN category Manufacturer source for the fiducial markers nanoprobes This data item is the primary key of the category. Listing of image files (figures) associated with an EMDB entry Example 1 <PDBx:em_figure_depositor_infoCategory> <PDBx:em_figure_depositor_info id="1"> <PDBx:details xsi:nil="true" /> <PDBx:experiment_id>1</PDBx:experiment_id> <PDBx:upload_file_name>groel-chimera-image.png</PDBx:upload_file_name> </PDBx:em_figure_depositor_info> </PDBx:em_figure_depositor_infoCategory> Details about the image file. This data item optionally associates an image (figure) with an experiment. The name of the image file associated with the map entry This data item is the unique identifier for an image file. Information about the final image classification Example 1 <PDBx:em_final_classificationCategory> <PDBx:em_final_classification id="1"> <PDBx:image_processing_id>1</PDBx:image_processing_id> </PDBx:em_final_classification> </PDBx:em_final_classificationCategory> The average number of images per class in the final 2D classification Additional details about the final 2D classification The final 2D classification had a highly asymmetric distribution owing to preferred orientations in the prepared specimen Foreign key to the EM_IMAGE_PROCESSING category The number of classes used in the final 2D classification Space (2D/3D) for the classification. Primary key Description of sectioning by focused_ion_beam Current of the ion beam, in nanoamperes (nA) Additional details about FIB milling ions per sq centimetre per second Milling time in seconds (is seconds most appropriate unit?) Foreign key relationship to the EM TOMOGRAPHY SPECIMEN category Final sample thickness Initial sample thickness The instrument used for focused ion beam sectioning FEI Quanta FIB The ion source used to ablate the specimen gallium ion gold ion iridium ion Temperature of the sample during milling, in degrees Kelvin 100 Voltage applied to the ion source, in kilovolts 30 This data item is the primary key of the category. Data items in the EMD_VALIDATION_FSC_CURVE category record details of the Fourier Shell Correlation (FSC) curve file. Example 1 <PDBx:em_fsc_curveCategory> <PDBx:em_fsc_curve id="1"> <PDBx:file>fsc_curve.txt</PDBx:file> </PDBx:em_fsc_curve> </PDBx:em_fsc_curveCategory> Details about the FSC file. FSC file name. emd-5470-fsc.txt This data item provides a unique identifier for each archived FSC curve. Data items describing glow discharge pretreatment for an EM grid Example 1 <PDBx:em_grid_pretreatmentCategory> <PDBx:em_grid_pretreatment id="1"> <PDBx:sample_support_id>1</PDBx:sample_support_id> <PDBx:time>12</PDBx:time> <PDBx:type>GLOW DISCHARGE</PDBx:type> </PDBx:em_grid_pretreatment> </PDBx:em_grid_pretreatmentCategory> The atmosphere used for glow discharge of the em grid. AIR AMYLAMINE Pressure of the glow discharge chamber, in pascals Pointer to EM SAMPLE SUPPORT Time period for glow discharge of the em grid, in seconds Type of grid pretreatment This data item is the primary key of the category. Data items in the EM_HELICAL_ENTITY category record details for a helical or filament type of assembly component. The angular rotation per helical subunit in degrees. -34.616000 The axial rise per subunit in the helical assembly. 17.400000 Symmetry of the helical axis, either cyclic (Cn) or dihedral (Dn), where n>=1. C1 D2 C7 Any other details regarding the helical assembly Dihedral symmetry Value should be YES if a the filament has two-fold symmetry perpendicular to the helical axis. The value of attribute entity_assembly_id in category em_helical_entity identifies a particular assembly component. This data item is a pointer to attribute id in category em_entity_assembly in the EM_ENTITY_ASSEMBLY category. Handedness of the helix: right handed or left handed Right Left The value of attribute id in category em_helical_entity must uniquely identify a set of the filament parameters for this assembly component. The value of attribute reconstruction_id in category em_helical_entity identifies a particular reconstruction. This data item is a pointer to attribute id in category em_image_processing. Description of high pressure freezing Additional details about high pressure freezing. High pressure freezing chamber was 250 um thick, 3.0 mm diameter, with central cavities 1.5 mm x 0.5 mm x 200 um deep. The chamber was pre-coated with 0.5% lecithin in chloroform. Foreign key relationship to the EMD SPECIMEN category The instrument used for high pressure freezing. Leica EM HP100 This data item is the primary key of the category. Data items in the EM_IMAGE_PROCESSING category record details of the EM image processing procedure. Example 1 <PDBx:em_image_processingCategory> <PDBx:em_image_processing id="1" image_recording_id="1"> <PDBx:details>The selected images were high-pass filtered and normalized</PDBx:details> </PDBx:em_image_processing> </PDBx:em_image_processingCategory> Method details. The selected images were high-pass filtered and normalized This data item provides a unique identifier for each data processing block. Foreign key to the EM_IMAGE_RECORDING Data items in the EM_IMAGE_RECORDING category record details of the image recording (either film/microdensitometer or electronic detector) and parameters for image digitization. Example 1 - images collected on film <PDBx:em_image_recordingCategory> <PDBx:em_image_recording id="1" imaging_id="1"> <PDBx:avg_electron_dose_per_image>0.9</PDBx:avg_electron_dose_per_image> <PDBx:film_or_detector_model>GENERIC FILM</PDBx:film_or_detector_model> <PDBx:num_diffraction_images>48</PDBx:num_diffraction_images> </PDBx:em_image_recording> </PDBx:em_image_recordingCategory> The average exposure time for each image. 2.0 The electron dose received by the specimen per image (electrons per square angstrom). 30.0 Any additional details about image recording. Images were collected in movie-mode at 17 frames per second The detector mode used during image recording. The detector type used for recording images. Usually film or CCD camera. The number of diffraction images collected. Number of grids in the microscopy session The number of micrograph images collected. The item attribute id in category em_image_recording uniquely identifies a set of recorded images. This data item the id of the microscopy settings used in the imaging. Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_image_scansCategory> <PDBx:em_image_scans id="2"> <PDBx:details xsi:nil="true" /> <PDBx:entry_id>1DYL</PDBx:entry_id> <PDBx:number_digital_images>48</PDBx:number_digital_images> <PDBx:od_range xsi:nil="true" /> <PDBx:quant_bit_size xsi:nil="true" /> <PDBx:sampling_size xsi:nil="true" /> <PDBx:scanner_model xsi:nil="true" /> </PDBx:em_image_scans> </PDBx:em_image_scansCategory> This data item is a pointer to attribute id in category citation in the CITATION category. Any additional details about image recording. height of scanned image width of scanned image This data item is a pointer to attribute id in category entry in the ENTRY category. Total number of time-slice (movie) frames taken per image. 10 The number of real images. The optical density range (OD=-log 10 transmission). To the eye OD=1 appears light grey and OD=3 is opaque. 1.4 The number of bits per pixel. 8 The sampling step size (microns) set on the scanner. The scanner model. Range of time-slice (movie) frames used for the reconstruction. 2-10 The value of attribute id in category em_image_scans must uniquely identify the images scanned. foreign key linked to _em_image_recording Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_imagingCategory> <PDBx:em_imaging entry_id="1DYL" id="1"> <PDBx:accelerating_voltage>200</PDBx:accelerating_voltage> <PDBx:calibrated_magnification xsi:nil="true" /> <PDBx:date>1998-15-06</PDBx:date> <PDBx:details xsi:nil="true" /> <PDBx:detector_distance xsi:nil="true" /> <PDBx:electron_source>FEG</PDBx:electron_source> <PDBx:energy_filter xsi:nil="true" /> <PDBx:energy_window xsi:nil="true" /> <PDBx:illumination_mode>bright field</PDBx:illumination_mode> <PDBx:microscope_model>FEI/PHILIPS CM200 FEG</PDBx:microscope_model> <PDBx:mode>low dose</PDBx:mode> <PDBx:nominal_cs>2.0</PDBx:nominal_cs> <PDBx:nominal_defocus_max>7600</PDBx:nominal_defocus_max> <PDBx:nominal_defocus_min>975</PDBx:nominal_defocus_min> <PDBx:nominal_magnification>50000</PDBx:nominal_magnification> <PDBx:recording_temperature_maximum xsi:nil="true" /> <PDBx:recording_temperature_minimum xsi:nil="true" /> <PDBx:sample_support_id>1</PDBx:sample_support_id> <PDBx:specimen_holder_model>gatan 626-0300</PDBx:specimen_holder_model> <PDBx:specimen_holder_type>cryotransfer</PDBx:specimen_holder_type> <PDBx:temperature>95</PDBx:temperature> <PDBx:tilt_angle_max>0</PDBx:tilt_angle_max> <PDBx:tilt_angle_min>0</PDBx:tilt_angle_min> </PDBx:em_imaging> </PDBx:em_imagingCategory> A value of accelerating voltage (in kV) used for imaging. 300 microscope alignment procedure astigmatism The open diameter of the c2 condenser lens, in microns. The maximum defocus value of the objective lens (in nanometers) used to obtain the recorded images. 5000 The minimum defocus value of the objective lens (in nanometers) used to obtain the recorded images. 1200 The magnification value obtained for a known standard just prior to, during or just after the imaging experiment. 61200 This data item is a pointer to attribute id in category citation in the CITATION category. Cryogen type used to maintain the specimen stage temperature during imaging in the microscope. Date (YYYY-MM-DD) of imaging experiment or the date at which a series of experiments began. 2001-05-08 Any additional imaging details. Preliminary grid screening was performed manually. The camera length (in millimeters). The camera length is the product of the objective focal length and the combined magnification of the intermediate and projector lenses when the microscope is operated in the diffraction mode. The value of attribute detector_id in category em_imaging must uniquely identify the type of detector used in the experiment. electron beam tilt params The electron dose received by the specimen (electrons per square angstrom). 0.9 The source of electrons. The electron gun. The type of energy filter spectrometer apparatus. FEI The energy filter range in electron volts (eV)set by spectrometer. 0 - 15 The mode of illumination. This data item is a pointer to attribute id in category em_microscope in the EM_MICROSCOPE category. The name of the model of microscope. The mode of imaging. The spherical aberration coefficient (Cs) in millimeters, of the objective lens. 2.0 The maximum defocus value of the objective lens (in nanometers) used to obtain the recorded images. 5000 The minimum defocus value of the objective lens (in nanometers) used to obtain the recorded images. 1200 The magnification indicated by the microscope readout. 60000 The specimen temperature maximum (degrees Kelvin) for the duration of imaging. The specimen temperature minimum (degrees Kelvin) for the duration of imaging. residual tilt of the electron beam This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. The value of attribute scans_id in category em_imaging must uniquely identify the image_scans used in the experiment. The name of the model of specimen holder used during imaging. The type of specimen holder used during imaging. cryo Foreign key to the EM_SPECIMEN category The mean specimen stage temperature (degrees Kelvin) during imaging in the microscope. 70 The maximum angle at which the specimen was tilted to obtain recorded images. 70 The minimum angle at which the specimen was tilted to obtain recorded images. -70 This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_imaging must uniquely identify each imaging experiment. Description of a few specialist optics apparatus Example 1 <PDBx:em_imaging_opticsCategory> <PDBx:em_imaging_optics id="1" imaging_id="1"> <PDBx:chr_aberration_corrector>CEOS manufactured Cc corrector</PDBx:chr_aberration_corrector> <PDBx:energyfilter_lower>0</PDBx:energyfilter_lower> <PDBx:energyfilter_name>FEI</PDBx:energyfilter_name> <PDBx:energyfilter_upper>15</PDBx:energyfilter_upper> </PDBx:em_imaging_optics> </PDBx:em_imaging_opticsCategory> Chromatic aberration corrector information CEOS manufactured Cc corrector Details on the use of the phase plate specified in attribute phase_plate in category em_imaging_optics Phase plate evolution varied between different microscopes used to collect data but positions were shifted once phase evolution progressed past 120 degrees. The energy filter range lower value in electron volts (eV) set by spectrometer. 0 The type of energy filter spectrometer GIF 200 The energy filter range slit width in electron volts (eV). 35 The energy filter range upper value in electron volts (eV) set by spectrometer. 15 Phase plate information Zernike phase plate Spherical aberration corrector information Microscope was modified with a Cs corrector with two hexapole elements. Primary key Foreign key to the EM IMAGING category Listing of all layer line files associated with the EM entry Example 1 <PDBx:em_interpret_figureCategory> <PDBx:em_interpret_figure id="1"> <PDBx:details xsi:nil="true" /> <PDBx:file>emd-1234.png</PDBx:file> </PDBx:em_interpret_figure> </PDBx:em_interpret_figureCategory> Details about the image file. The name of the image file associated with the map entry This data item is the unique identifier for the image file. Listing of all layer line files associated with the EM entry Example 1 <PDBx:em_layer_linesCategory> <PDBx:em_layer_lines experiment_id="1" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:file>emd-1234-sf.cif</PDBx:file> </PDBx:em_layer_lines> </PDBx:em_layer_linesCategory> Details about the layer line file. The name of the layer line file associated with the map entry This data item is a pointer to the EM EXPERIMENT category. This data item is the unique identifier for the layer line file. Listing of layer line files associated with the EM entry Example 1 <PDBx:em_layer_lines_depositor_infoCategory> <PDBx:em_layer_lines_depositor_info id="1"> <PDBx:details xsi:nil="true" /> <PDBx:experiment_id>1</PDBx:experiment_id> <PDBx:upload_file_name>emd-1234-ll.cif</PDBx:upload_file_name> </PDBx:em_layer_lines_depositor_info> </PDBx:em_layer_lines_depositor_infoCategory> Details about the layer line file. This data item is a pointer to the EMD_STRUCT category. The name of the layer line file associated with the map entry This data item is the unique identifier for the layer line file. Data items in the EMD_MAP category record parameters of the CCP4 binary-format map file header (see ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf), parameters derived from the map header, pixel size, contour level, and annotation details from the depositor. The map is a three-dimensional array of data-values of the same data-type. Important parameters are data-type and array size in three dimensions (i.e. the number of columns, rows and sections). Columns are the fastest changing, followed by rows and sections. Example 1 - based on map entry EMD-5001 <PDBx:em_mapCategory> <PDBx:em_map entry_id="1ABC" id="1"> <PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details> <PDBx:axis_order_fast>X</PDBx:axis_order_fast> <PDBx:axis_order_medium>Y</PDBx:axis_order_medium> <PDBx:axis_order_slow>Z</PDBx:axis_order_slow> <PDBx:cell_a>212.0</PDBx:cell_a> <PDBx:cell_alpha>90.0</PDBx:cell_alpha> <PDBx:cell_b>212.0</PDBx:cell_b> <PDBx:cell_beta>90.0</PDBx:cell_beta> <PDBx:cell_c>212.0</PDBx:cell_c> <PDBx:cell_gamma>90.0</PDBx:cell_gamma> <PDBx:data_type>Image stored as Reals</PDBx:data_type> <PDBx:dimensions_col>200</PDBx:dimensions_col> <PDBx:dimensions_row>200</PDBx:dimensions_row> <PDBx:dimensions_sec>200</PDBx:dimensions_sec> <PDBx:format>CCP4</PDBx:format> <PDBx:origin_col>-100</PDBx:origin_col> <PDBx:origin_row>-100</PDBx:origin_row> <PDBx:origin_sec>-100</PDBx:origin_sec> <PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x> <PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y> <PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z> <PDBx:size_kb>32002</PDBx:size_kb> <PDBx:spacing_x>200</PDBx:spacing_x> <PDBx:spacing_y>200</PDBx:spacing_y> <PDBx:spacing_z>200</PDBx:spacing_z> <PDBx:statistics_average>0.0668982</PDBx:statistics_average> <PDBx:statistics_maximum>2.42436</PDBx:statistics_maximum> <PDBx:statistics_minimum>-0.965912</PDBx:statistics_minimum> <PDBx:statistics_std>0.23771</PDBx:statistics_std> <PDBx:symmetry_space_group>1</PDBx:symmetry_space_group> </PDBx:em_map> </PDBx:em_mapCategory> map annotation details The map axis that corresponds to Columns. (CCP4 HEADER WORD 17 MAPC 1=x, 2=y, 3=z) The map axis that corresponds to Rows. (CCP4 map header word 18 MAPR 1=x, 2=y, 3=z) The map axis that corresponds to Sections. (CCP4 map header word 19 MAPS 1=x, 2=y, 3=z) Map unit cell length parameter a. (CCP4 map header word 11) Value of map unit cell angle parameter alpha in degrees. (CCP4 map header word 14) Map unit cell length parameter b. (CCP4 map header word 12) Value of map unit cell angle parameter beta in degrees. (CCP4 map header word 15) Map unit cell length parameter c. (CCP4 map header word 13) Value of map unit cell angle parameter gamma in degrees. (CCP4 map header word 16) recommended contour level for viewing the map source of the recommended contour level author The map data_type describes the data structure of the map voxels. (CCP4 map header word 4 MODE) EMDB currently holds MODE=0,1,and 2 maps; the majority are MODE=2. MAPS with MODES other than 2 and 0 may not work in CCP4 programs. MODE = 0: 8 bits, density stored as a signed byte (-128 to 127, ISO/IEC 10967) MODE = 1: 16 bits, density stored as a signed integer (-32768 to 32767, ISO/IEC 10967) MODE = 2: 32 bits, density stored as a floating point number (IEEE 754) The number of columns in the map. (CCP4 map header word 1 NC) The number of rows in the map. (CCP4 map header word 2 NR) The number of sections in the map. (CCP4 map header word 3 NS) map file endian type Map file name. emd_5470.map.gz map format text stored in the label field of the CCP4 map header (WORDS 57-256) The final column position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived = .origin_col + .dimensions_col -1) The final row position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived = .origin_row + .dimensions_row -1) The final section position of the map relative to the Cartesian coordinate origin in voxel grid units. (derived -- .origin_sec + .dimensions_sec -1) The position of the first column of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 5 NCSTART) The position of the first row of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 6 NRSTART) The position of the first section of the map relative to the Cartesian coordinate origin in voxel grid units. (CCP4 map header word 7 NSSTART) Identifies the archive file partition number of a primary map, half map, additional map, or mask. The length in Angstroms of one voxel along the X axis. The length in Angstroms of one voxel along the Y axis. The length in Angstroms of one voxel along the Z axis. map storage size in Kilobytes (before compression) The number of intervals per cell repeat in X. (CCP4 map header word 8 NX) The number of intervals per cell repeat in Y. (CCP4 map header word 9 NY) The number of intervals per cell repeat in Z. (CCP4 map header word 10 NZ) Mean (average) density value of the map. Maximum density value of the map. Minimum density value of the map. The standard deviation of the map density values. The space group number for the map. The value is 1 unless the sample is crystalline. (CCP4 map header word 23 ISPG) map format This data item is a pointer to the ENTRY category. Unique id for the EMD_MAP category. Data items in the EM_MAP_DEPOSITOR INFO category record map parameters that are provided by the depositor Example 1 - based on map entry EMD-5001 <PDBx:em_map_depositor_infoCategory> <PDBx:em_map_depositor_info entry_id="D_10005049" id="1"> <PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details> <PDBx:contour_level>5.0</PDBx:contour_level> <PDBx:experiment_id xsi:nil="true" /> <PDBx:map_type>primary</PDBx:map_type> <PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x> <PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y> <PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z> <PDBx:upload_file_name>GroelD7.mrc.gz</PDBx:upload_file_name> <PDBx:upload_format>CCP4/MRC</PDBx:upload_format> </PDBx:em_map_depositor_info> </PDBx:em_map_depositor_infoCategory> map annotation details recommended contour level for viewing the map This data item optionally associates a map with a data item in the EM_EXPERIMENT category. Primary map or additional map classification. The length in Angstroms of one voxel along the X axis. The length in Angstroms of one voxel along the Y axis. The length in Angstroms of one voxel along the Z axis. The name of a file containing the map. map format This data item is a pointer to the ENTRY category. Unique identifier for each map listed. Data items in the EM_MASK_DEPOSITOR_INFO category record mask parameters that are provided by the depositor Example 1 - based on map entry EMD-5001 <PDBx:em_mask_depositor_infoCategory> <PDBx:em_mask_depositor_info id="1"> <PDBx:annotation_details>D7 structure of Groel at 4.2 Angstrom resolution</PDBx:annotation_details> <PDBx:contour_level>5.0</PDBx:contour_level> <PDBx:pixel_spacing_x>1.06</PDBx:pixel_spacing_x> <PDBx:pixel_spacing_y>1.06</PDBx:pixel_spacing_y> <PDBx:pixel_spacing_z>1.06</PDBx:pixel_spacing_z> <PDBx:upload_file_name>GroelD7.mrc.gz</PDBx:upload_file_name> <PDBx:upload_format>CCP4/MRC</PDBx:upload_format> </PDBx:em_mask_depositor_info> </PDBx:em_mask_depositor_infoCategory> map annotation details recommended contour level for viewing the map The length in Angstroms of one voxel along the X axis. The length in Angstroms of one voxel along the Y axis. The length in Angstroms of one voxel along the Z axis. The name of a file containing the map. map format Unique identifier for each map listed. List of EMD entries made obsolete by this entry. Dated when the entry made obsolete the other entry Details Entry made obsolete Primary key Data items in this category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_particle_selectionCategory> <PDBx:em_particle_selection id="1" image_processing_id="1"> <PDBx:details xsi:nil="true" /> <PDBx:method>INTERACTIVE</PDBx:method> <PDBx:num_particles_selected>5267</PDBx:num_particles_selected> </PDBx:em_particle_selection> </PDBx:em_particle_selectionCategory> Any additional details used for selecting particles negative monitor contrast facilitated particle picking The method used for selecting particles particles picked interactively from monitor The number of particles selected from the projection set of images. 840 Description of reference model used for particle selection Ordinal identifier The value of attribute image_processing_id in category em_particle_selection points to the EM_IMAGE_PROCESSING category. Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to and upon loading onto grid support. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_sample_preparationCategory> <PDBx:em_sample_preparation entry_id="1DYL" id="1"> <PDBx:_2d_crystal_grow_id xsi:nil="true" /> <PDBx:buffer_id>1</PDBx:buffer_id> <PDBx:ph>7.6</PDBx:ph> <PDBx:sample_concentration>5</PDBx:sample_concentration> <PDBx:support_id>1</PDBx:support_id> </PDBx:em_sample_preparation> </PDBx:em_sample_preparationCategory> This data item is a pointer to attribute id in category em_2d_crystal_grow in the 2D_CRYSTAL_GROW category. This data item is a pointer to attribute id in category em_buffer in the BUFFER category. Details of the specimen preparation 1 Detergent-solubilized particles eluted from the cation-exchange column were directly adsorbed for 1 min to parlodion carbon-coated copper grids rendered hydrophilic by glow discharge at low pressure in air. Grids were washed with 4 drops of double-distilled water and stained with 2 drops of 0.75% uranyl formate. 2 Selectively stained by injection of horseradish peroxidase, embedded in Spurr's resin and cut into 2-3 um thick sections. 3 S. cerevisiae PDC was purified to near homogeneity from baker's yeast by modification of a published procedure. Highly purified E1 was obtained by resolution of PDC with 2 M NaCl at pH 7.3 followed by FPLC on a Superdex 200 column. The weight-average molecular weight of the PDC was determined by light scattering measurement to be ~8 x 106. On the basis of the known molecular weight of the complex and its component enzymes and the experimentally determined polypeptide chain ratios of E2/BP/E3, we estimated that the subunit composition of the S. cerevisiae PDC is ~24 E1 tetramers, 60 E2 monomers, 12 BP monomers, and 8 E3 dimers. Sufficient E1 was added to a sample of the PDC preparation to increase the molar ratio of E1/E2 core to 60:1. 4 embedded in vitreous ice. This data item is a pointer to attribute id in category entity_assembly in the em_entity_assembly category. The pH value of the observed sample buffer. 5.5 The value of the concentration (mg per milliliter) of the complex in the sample. 1.35 This data item is a pointer to attribute id in category em_sample_support in the EM_SAMPLE_SUPPORT category. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category em_sample_preparation must uniquely identify the sample preparation. Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_sample_supportCategory> <PDBx:em_sample_support id="1"> <PDBx:details>GLOW DISCHARGED 120 seconds</PDBx:details> <PDBx:film_material>HOLEY CARBON</PDBx:film_material> <PDBx:grid_material>COPPER</PDBx:grid_material> <PDBx:grid_mesh_size>400</PDBx:grid_mesh_size> </PDBx:em_sample_support> </PDBx:em_sample_supportCategory> This data item is a pointer to attribute id in category citation in the CITATION category. Any additional details concerning the sample support. The grid was coated with gold prior to use The support material covering the em grid. The name of the material from which the grid is made. The value of the mesh size (divisions per inch) of the em grid. 400 A description of the grid type. A description of the method used to produce the support film. 1%formvar in chloroform cast on distilled water A description of the grid plus support film pretreatment. glow-discharged for 30 sec in argon The value of attribute id in category em_sample_support must uniquely identify the sample support. This data item is a pointer to attribute id in category em_sample_preparation in the EM_SPECIMEN category. Data items related to shadowing of an EM specimen Example 1 <PDBx:em_shadowingCategory> <PDBx:em_shadowing id="1" specimen_id="1"> <PDBx:angle>45</PDBx:angle> <PDBx:details>shadowing was used to create a platinum replica</PDBx:details> <PDBx:material>Platinum</PDBx:material> <PDBx:thickness>3</PDBx:thickness> </PDBx:em_shadowing> </PDBx:em_shadowingCategory> The shadowing angle (degrees) 20 Additional details about specimen shadowing rotary shadowing directional shadowing shadowing was used to create a carbon replica The material used in the shadowing. Platinum Thickness of the deposited shadow coat, in Angstroms. This data item is the primary key of the category. Foreign key relationship to the EMD SPECIMEN category Data items in the EM_SINGLE_PARTICLE_ENTITY category provide the details of the symmetry for a single particle entity type. Example <PDBx:em_single_particle_entityCategory> <PDBx:em_single_particle_entity id="1" image_processing_id="1"> <PDBx:point_symmetry>I</PDBx:point_symmetry> </PDBx:em_single_particle_entity> </PDBx:em_single_particle_entityCategory> This data item is a pointer to attribute id in category entry in the ENTRY category. Point symmetry symbol, either Cn, Dn, T, O, or I The single particle symmetry type. Unique category label. pointer to attribute id in category em_image_processing. Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used. Example 1 <PDBx:em_softwareCategory> <PDBx:em_software id="1"> <PDBx:category>IMAGE ACQUISITION</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>Leginon</PDBx:name> <PDBx:version>1.3</PDBx:version> </PDBx:em_software> <PDBx:em_software id="2"> <PDBx:category>PARTICLE SELECTION</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>X3D</PDBx:name> <PDBx:version xsi:nil="true" /> </PDBx:em_software> <PDBx:em_software id="3"> <PDBx:category>BACKGROUND MASKING</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>bsoft</PDBx:name> <PDBx:version>1.1</PDBx:version> </PDBx:em_software> <PDBx:em_software id="4"> <PDBx:category>RECONSTRUCTION</PDBx:category> <PDBx:details>em3dr2 -low 20</PDBx:details> <PDBx:name>EM2DR2</PDBx:name> <PDBx:version>3.2</PDBx:version> </PDBx:em_software> <PDBx:em_software id="5"> <PDBx:category>EULER ASSIGNMENT</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>erandom</PDBx:name> <PDBx:version xsi:nil="true" /> </PDBx:em_software> <PDBx:em_software id="6"> <PDBx:category>CTF CORRECTION</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>bctf</PDBx:name> <PDBx:version xsi:nil="true" /> </PDBx:em_software> <PDBx:em_software id="7"> <PDBx:category>MODEL FITTING</PDBx:category> <PDBx:details xsi:nil="true" /> <PDBx:name>chimera</PDBx:name> <PDBx:version>1.6</PDBx:version> </PDBx:em_software> </PDBx:em_softwareCategory> The purpose of the software. Details about the software used. EMAN2 e2boxer.py was used to automatically select particle images. pointer to attribute id in category em_3d_fitting in the EM_3D_FITTING category. pointer to attribute id in category em_image_processing in the EM_IMAGE_PROCESSING category. pointer to attribute id in category em_imaging in the EM_IMAGING category. The name of the software package used, e.g., RELION. Depositors are strongly encouraged to provide a value in this field. EMAN Imagic Spider Bsoft UCSF-Chimera The version of the software. 9.03 2.1 Unique identifier for each software description. Data items in the EMD_SPECIMEN category record details about specimens prepared for imaging by electron microscopy. Example 1 -- based on PDB 2FL8 <PDBx:em_specimenCategory> <PDBx:em_specimen experiment_id="1" id="1"> <PDBx:embedding_applied>NO</PDBx:embedding_applied> <PDBx:shadowing_applied>NO</PDBx:shadowing_applied> <PDBx:staining_applied>NO</PDBx:staining_applied> <PDBx:vitrification_applied>YES</PDBx:vitrification_applied> </PDBx:em_specimen> </PDBx:em_specimenCategory> The concentration (in milligrams per milliliter, mg/ml) of the complex in the sample. 1.35 A description of any additional details of the specimen preparation. This sample was monodisperse. Au was deposited at a 30 degree angle to 15 nm thickness. Colloidal gold particles were deposited by dipping into dilute solution. The specimen was frozen at high pressure using the bal-tec hpm 010 instrument. The embedded sample was sectioned at 100 K to 50 nm final thickness. 'YES' indicates that the specimen has been embedded. 'YES' indicates that the specimen has been shadowed. 'YES' indicates that the specimen has been stained. 'YES' indicates that the specimen was vitrified by cryopreservation. Pointer to attribute id in category em_experiment. The item attribute id in category em_specimen uniquely identifies a specimen along with its preparation methods. Staining category Example 1 <PDBx:em_stainingCategory> <PDBx:em_staining id="1"> <PDBx:material>Uranyl Acetate</PDBx:material> <PDBx:specimen_id>1</PDBx:specimen_id> <PDBx:type>NEGATIVE</PDBx:type> </PDBx:em_staining> </PDBx:em_stainingCategory> Staining procedure used in the specimen preparation. Negatively stained EM specimens were prepared using a carbon-sandwich technique and uranyl-formate stain. The staining material. Uranyl Acetate Foreign key relationship to the EMD SPECIMEN category type of staining This data item is the primary key of the category. The startup model employed to begin refinement of the parameters for a 3DEM reconstruction Example 1 -- based on PDB 3IYD <PDBx:em_start_modelCategory> <PDBx:em_start_model id="1" image_processing_id="1"> <PDBx:details>a map created from PDB entry 3DXJ was gaussian blurred to 60 Angstroms</PDBx:details> <PDBx:pdb_id>3DXJ</PDBx:pdb_id> <PDBx:type>PDB ENTRY</PDBx:type> </PDBx:em_start_model> </PDBx:em_start_modelCategory> Any additional details about generating the startup model EMDB id of the map used as the startup model Description of the "in silico" model used to generate the startup model Tilt angle for the 1st image set of the orthogonal tilt pairs -45 Tilt angle for the 2nd image set of the orthogonal tilt pairs 45 number of images used to generate the orthogonal tilt startup model 40 Description of other method/source used to generate the startup model PDB id of the model coordinates used to generate the startup model Angular difference between the conical tilt images used to generate the startup model 60 number of images used to generate the random conical tilt startup model 40 Type of startup model (map density) used to initiate the reconstruction Primary key Foreign key to the EM_IMAGE_PROCESSING category Listing of all structure factor files associated with the EM entry Example 1 <PDBx:em_structure_factorsCategory> <PDBx:em_structure_factors experiment_id="1" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:file>emd-1234-sf.cif</PDBx:file> </PDBx:em_structure_factors> </PDBx:em_structure_factorsCategory> Details about the structure factor file. The name of the structure factor file associated with the map entry This data item is a pointer to the EM EXPERIMENT category. This data item is the unique identifier for the structure factor file. Structure factor files associated with the EM entry Example 1 <PDBx:em_structure_factors_depositor_infoCategory> <PDBx:em_structure_factors_depositor_info id="1"> <PDBx:details xsi:nil="true" /> <PDBx:experiment_id>1</PDBx:experiment_id> <PDBx:upload_file_name>emd-1234-sf.cif</PDBx:upload_file_name> </PDBx:em_structure_factors_depositor_info> </PDBx:em_structure_factors_depositor_infoCategory> Details about the structure factor file. This data item is an optional pointer to the EM_EXPERIMENT category. The name of the structure factor file associated with the map entry This data item is the unique identifier for the structure factor file. List of newer entries that replace this entry. Dated when the entry made supersede the other entry Details Newer entry that replaces this entry Primary key Data items to describe films supporting the specimen Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_support_filmCategory> <PDBx:em_support_film id="1"> <PDBx:material>CARBON</PDBx:material> </PDBx:em_support_film> </PDBx:em_support_filmCategory> The support material covering the em grid. Pointer to EM SAMPLE SUPPORT Thickness of the support film, in Angstroms The topology of the material from which the grid is made. This data item is the primary key of the category. Microscopy parameters only relevant for tomography Example 1 <PDBx:em_tomographyCategory> <PDBx:em_tomography id="1" imaging_id="1"> <PDBx:axis1_angle_increment>2</PDBx:axis1_angle_increment> <PDBx:axis1_max_angle>70.</PDBx:axis1_max_angle> <PDBx:axis1_min_angle>-70.</PDBx:axis1_min_angle> <PDBx:axis2_angle_increment>2</PDBx:axis2_angle_increment> <PDBx:axis2_max_angle>70.</PDBx:axis2_max_angle> <PDBx:axis2_min_angle>-70.</PDBx:axis2_min_angle> <PDBx:dual_tilt_axis_rotation>90.</PDBx:dual_tilt_axis_rotation> </PDBx:em_tomography> </PDBx:em_tomographyCategory> The angle increment of specimen tilting to obtain the recorded images (axis 1). 2 The maximum angle at which the specimen was tilted to obtain recorded images (axis 1). 70 The minimum angle at which the specimen was tilted to obtain recorded images (axis 1). -70 The angle increment of specimen tilting to obtain the recorded images (axis 1). 2 The maximum angle at which the specimen was tilted to obtain recorded images (axis 1). 70 The minimum angle at which the specimen was tilted to obtain recorded images (axis 1). -70 Angular difference between axis1 and axis2 in degrees Primary key Foreign key to the EM IMAGING category Description specimen preparation for imaging using tomography. The type of cryo-protectant used during specimen preparation. 2% glycerol Any additional details about specimen preparation. Axonemes were mixed with 15-nm colloidal gold suspension conjugated with BSA. Suspended axonemes plus colloidal gold were loaded onto grids and plunge-frozen in liquid ethane with a Leica EM GP automated plunge-freezing device. 'YES' indicates that fiducial markers were used in the specimen preparation 'YES' indicates that high pressure freezing was used in the specimen preparation The type of sectioning performed during specimen preparation. Foreign key relationship to the EMD SPECIMEN category This data item is the primary key of the category. Description of sectioning by ultramicrotomy Additional details about the ultramicrotomy sample preparation Foreign key relationship to the EMD SPECIMEN category Final thickness of the sectioned sample, in nanometers 60 Ultramicrotome instrument used for sectioning Leica EM UC7 Temperature of the sample during microtome sectioning, in degrees Kelvin 100 This data item is the primary key of the category. Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus. Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_virus_entityCategory> <PDBx:em_virus_entity entity_assembly_id="1" id="1"> <PDBx:empty>NO</PDBx:empty> <PDBx:enveloped>YES</PDBx:enveloped> <PDBx:ictvdb_id>00.073.0.01.023</PDBx:ictvdb_id> <PDBx:virus_host_category>VERTERBRATES</PDBx:virus_host_category> <PDBx:virus_host_species>HOMO SAPIENS</PDBx:virus_host_species> <PDBx:virus_isolate>STRAIN</PDBx:virus_isolate> <PDBx:virus_type>VIRUS</PDBx:virus_type> </PDBx:em_virus_entity> </PDBx:em_virus_entityCategory> Additional details about this virus entity Flag to indicate if the virus is empty or not. Flag to indicate if the virus is enveloped or not. The International Committee on Taxonomy of Viruses (ICTV) Taxon Identifier is the Virus Code used throughout the ICTV database (ICTVdb). The ICTVdb id is the appropriate identifier used by the International Committee on Taxonomy of Viruses Resource. Reference: Virus Taxonomy, Academic Press (1999). ISBN:0123702003. NOTE: ICTV no longer maintains ids; maintained for legacy only. NL-54 The host category description for the virus. ALGAE ARCHAEA BACTERIA(EUBACTERIA) FUNGI INVERTEBRATES PLANTAE (HIGHER PLANTS) PROTOZOA VERTEBRATES The host cell from which the virus was isolated. HELA CHO The host species from which the virus was isolated. homo sapiens gallus gallus The isolate from which the virus was obtained. The type of virus. This data item is a pointer to attribute id in category em_virus_entity in the ENTITY_ASSEMBLY category. Is the unique identifier for VIRUS_ENTITY category. Data items in this category record details of a virus entity. The NCBI taxonomy of the host species from which the virus was isolated. The host organism from which the virus was isolated. Homo sapiens Gallus gallus The strain of the host organism from which the virus was obtained, if relevant. DH5a BMH 71-18 Pointer to attribute id in category em_entity_assembly. Unique identifier for the virus natural host. Data items in the EMD_VIRUS_SHELL category record details of the viral shell number, shell diameter, and icosahedral triangulation number. Example 1 -- Bluetongue Virus <PDBx:em_virus_shellCategory> <PDBx:em_virus_shell entity_assembly_id="1" id="1"> <PDBx:diameter>348</PDBx:diameter> <PDBx:name>VP7 layer</PDBx:name> <PDBx:triangulation>13</PDBx:triangulation> </PDBx:em_virus_shell> <PDBx:em_virus_shell entity_assembly_id="1" id="2"> <PDBx:diameter>348</PDBx:diameter> <PDBx:name>VP3 layer</PDBx:name> <PDBx:triangulation>2</PDBx:triangulation> </PDBx:em_virus_shell> </PDBx:em_virus_shellCategory> The value of the diameter (in angstroms) for this virus shell. 524.0 The name for this virus shell. The triangulation number (T number) is a geometric concept that refers to the organisation of subunits within the icosahedron. The triangulation number, T is given by the relationship T= h*2 + hk +k*2, where h and k are positive integers which define the position of the five-fold vertex on the original hexagonal net. 27 The value of attribute entity_assembly_id in category em_virus_shell is a pointer to attribute id in category em_entity_assembly category. The value of attribute id in category em_em_virus_shell is a unique identifier for one virus shell. Data items in this category record details of a synthetic virus entity. The NCBI taxonomy of the host species from which the virus was isolated. The host organism from which the virus was isolated. Homo sapiens Gallus gallus The strain of the host organism from which the virus was obtained, if relevant. DH5a BMH 71-18 Pointer to attribute id in category em_entity_assembly. Unique identifier for the virus natural host. Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_vitrificationCategory> <PDBx:em_vitrification id="1"> <PDBx:cryogen_name>ETHANE</PDBx:cryogen_name> <PDBx:details> SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626-0300 CRYOTRANSFER HOLDER.</PDBx:details> <PDBx:entry_id>1DYL</PDBx:entry_id> <PDBx:humidity>90</PDBx:humidity> <PDBx:instrument xsi:nil="true" /> <PDBx:method>PLUNGE VITRIFICATION</PDBx:method> <PDBx:sample_preparation_id>1</PDBx:sample_preparation_id> <PDBx:temp>95</PDBx:temp> <PDBx:time_resolved_state xsi:nil="true" /> </PDBx:em_vitrification> </PDBx:em_vitrificationCategory> The temperature (in degrees Kelvin) of the sample just prior to vitrification. 298 This data item is a pointer to attribute id in category citation in the CITATION category. This is the name of the cryogen. Any additional details relating to vitrification. Vitrification carried out in argon atmosphere. This data item is a pointer to attribute id in category entry in the ENTRY category. The humidity (%) in the vicinity of the vitrification process. 90 The type of instrument used in the vitrification process. The procedure for vitrification. plunge freezing This data item is a pointer to attribute id in category em_sample_preparation in the EM_SAMPLE_PREPARATION category. The vitrification temperature (in degrees Kelvin), e.g., temperature of the plunge instrument cryogen bath. 90 The length of time after an event effecting the sample that vitrification was induced and a description of the event. plunge 30 msec after spraying with effector The value of attribute id in category em_vitrification must uniquely identify the vitrification procedure. This data item is a pointer to attribute id in category em_specimen Volume selection in image processing Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:em_volume_selectionCategory> <PDBx:em_volume_selection id="1" image_processing_id="1"> <PDBx:details xsi:nil="true" /> <PDBx:method>INTERACTIVE</PDBx:method> <PDBx:num_volumes_extracted>5267</PDBx:num_volumes_extracted> </PDBx:em_volume_selection> </PDBx:em_volume_selectionCategory> Any additional details used for selecting volumes. negative monitor contrast facilitated volume picking The method used for selecting volumes. volumes picked interactively The number of tomograms used in the extraction/selection 20 The number of volumes selected from the projection set of images. 840 Description of reference model used for volume selection Ordinal identifier The value of attribute image_processing_id in category em_volume_selection points to the EM_IMAGE_PROCESSING category. Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entityCategory> <PDBx:entity id="1"> <PDBx:details> The enzymatically competent form of HIV protease is a dimer. This entity corresponds to one monomer of an active dimer.</PDBx:details> <PDBx:formula_weight>10916</PDBx:formula_weight> <PDBx:type>polymer</PDBx:type> </PDBx:entity> <PDBx:entity id="2"> <PDBx:details xsi:nil="true" /> <PDBx:formula_weight>762</PDBx:formula_weight> <PDBx:type>non-polymer</PDBx:type> </PDBx:entity> <PDBx:entity id="3"> <PDBx:details xsi:nil="true" /> <PDBx:formula_weight>18</PDBx:formula_weight> <PDBx:type>water</PDBx:type> </PDBx:entity> </PDBx:entityCategory> A description of special aspects of the entity. Formula mass in daltons of the entity. A description of the entity. Corresponds to the compound name in the PDB format. DNA (5'-D(*GP*(CH3)CP*GP*(CH3)CP*GP*C)-3') PROFLAVINE PROTEIN (DEOXYRIBONUCLEASE I (E.C.3.1.21.1)) Enzyme Commission (EC) number(s) 2.7.7.7 Number of entity molecules in the biological assembly. 1 2 3 Experimentally determined formula mass in daltons of the entity Method used to determine attribute pdbx_formula_weight_exptl in category entity. MASS SPEC Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN Description(s) of any chemical or post-translational modifications Details about any entity mutation(s). Y31H DEL(298-323) A place holder for the number of molecules of the entity in the entry. 1 2 3 An identifier for the parent entity if this entity is part of a complex entity. For instance a chimeric entity may be decomposed into several independent chemical entities where each component entity was obtained from a different source. 1 2 3 The value of attribute target_id in category entity points to a TARGETDB target idenitifier from which this entity was generated. The method by which the sample for the entity was produced. Entities isolated directly from natural sources (tissues, soil samples etc.) are expected to have further information in the ENTITY_SRC_NAT category. Entities isolated from genetically manipulated sources are expected to have further information in the ENTITY_SRC_GEN category. Defines the type of the entity. Polymer entities are expected to have corresponding ENTITY_POLY and associated entries. Non-polymer entities are expected to have corresponding CHEM_COMP and associated entries. Water entities are not expected to have corresponding entries in the ENTITY category. The value of attribute id in category entity must uniquely identify a record in the ENTITY list. Note that this item need not be a number; it can be any unique identifier. Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_keywordsCategory> <PDBx:entity_keywords entity_id="2"> <PDBx:text>natural product, inhibitor, reduced peptide</PDBx:text> </PDBx:entity_keywords> </PDBx:entity_keywordsCategory> PDB placeholder. Enzyme Commission (EC) number(s) 2.7.7.7 Entity fragment description(s). KLENOW FRAGMENT REPLICASE OPERATOR HAIRPIN C-TERMINAL DOMAIN Entity mutation description(s). Y31H DEL(298-323) Keywords describing this entity. polypeptide natural product polysaccharide This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the ENTITY_LINK category give details about the links between entities. A description of special aspects of a link between chemical components in the structure. The entity ID of the first of the two entities joined by the link. This data item is a pointer to attribute id in category entity in the ENTITY category. The entity ID of the second of the two entities joined by the link. This data item is a pointer to attribute id in category entity in the ENTITY category. For a polymer entity, the sequence number in the first of the two entities containing the link. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. For a polymer entity, the sequence number in the second of the two entities containing the link. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. This data item is a pointer to attribute id in category chem_link in the CHEM_LINK category. Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_name_comCategory> <PDBx:entity_name_com entity_id="1"> <PDBx:name>HIV-1 protease monomer</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="1"> <PDBx:name>HIV-1 PR monomer</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="2"> <PDBx:name>acetyl-pepstatin</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="2"> <PDBx:name>acetyl-Ile-Val-Asp-Statine-Ala-Ile-Statine</PDBx:name> </PDBx:entity_name_com> <PDBx:entity_name_com entity_id="3"> <PDBx:name>water</PDBx:name> </PDBx:entity_name_com> </PDBx:entity_name_comCategory> A common name for the entity. HIV protease monomer hemoglobin alpha chain 2-fluoro-1,4-dichloro benzene arbutin Provides the provenance of the name in the attribute name in category entity_name_com field This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_name_sysCategory> <PDBx:entity_name_sys entity_id="1"> <PDBx:name>EC 3.4.23.16</PDBx:name> </PDBx:entity_name_sys> <PDBx:entity_name_sys entity_id="2"> <PDBx:name>acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta</PDBx:name> </PDBx:entity_name_sys> <PDBx:entity_name_sys entity_id="3"> <PDBx:name>water</PDBx:name> </PDBx:entity_name_sys> </PDBx:entity_name_sysCategory> The systematic name for the entity. hydroquinone-beta-D-pyranoside EC 2.1.1.1 2-fluoro-1,4-dichlorobenzene The system used to generate the systematic name of the entity. Chemical Abstracts conventions enzyme convention Sigma catalog This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_polyCategory> <PDBx:entity_poly entity_id="1"> <PDBx:nstd_chirality>no</PDBx:nstd_chirality> <PDBx:nstd_linkage>no</PDBx:nstd_linkage> <PDBx:nstd_monomer>no</PDBx:nstd_monomer> <PDBx:type>polypeptide(L)</PDBx:type> <PDBx:type_details xsi:nil="true" /> </PDBx:entity_poly> </PDBx:entity_polyCategory> A flag to indicate whether the polymer contains at least one monomer unit with chirality different from that specified in attribute type in category entity_poly. A flag to indicate whether the polymer contains at least one monomer-to-monomer link different from that implied by attribute type in category entity_poly. A flag to indicate whether the polymer contains at least one monomer that is not considered standard. The number of monomers in the polymer. C-terminal cloning artifacts and/or HIS tag. HHHHHH N-terminal cloning artifacts and/or HIS tag. HHHHHH A code to indicate that this sequence should be assigned a PDB sequence reference. Y A flag to indicate that linking data is explicitly provided for this polymer in the PDBX_ENTITY_POLY_COMP_LINK_LIST category The sequence position in the database sequence at which the alignment with your sequence begins. 59 The sequence position in the database sequence at which the alignment with your sequence ends. 685 The identifier for this sequence in the sequence data base. P00730 The name of the sequence data base containing a database entry for this sequence. Enter UNP for a Uniport entry Enter SWS for a Swiss-Prot entry Enter GB for a GenBank entry Enter EMBL for an European Molecular Biology Laboratory entry Enter PIR for a Protein Information Resource entry Sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides. Non-standard amino acids/nucleotides are represented by their Chemical Component Dictionary (CCD) codes in parenthesis. Deoxynucleotides are represented by the specially-assigned 2-letter CCD codes in parenthesis, with 'D' prefix added to their ribonucleotide counterparts. For hybrid polymer, each residue is represented by the code of its individual type. A cyclic polymer is represented in linear sequence from the chosen start to end. A for Alanine or Adenosine-5'-monophosphate C for Cysteine or Cytidine-5'-monophosphate D for Aspartic acid E for Glutamic acid F for Phenylalanine G for Glycine or Guanosine-5'-monophosphate H for Histidine I for Isoleucine or Inosinic Acid L for Leucine K for Lysine M for Methionine N for Asparagine or Unknown ribonucleotide O for Pyrrolysine P for Proline Q for Glutamine R for Arginine S for Serine T for Threonine U for Selenocysteine or Uridine-5'-monophosphate V for Valine W for Tryptophan Y for Tyrosine (DA) for 2'-deoxyadenosine-5'-monophosphate (DC) for 2'-deoxycytidine-5'-monophosphate (DG) for 2'-deoxyguanosine-5'-monophosphate (DT) for Thymidine-5'-monophosphate (MSE) for Selenomethionine (SEP) for Phosphoserine (PTO) for Phosphothreonine (PTR) for Phosphotyrosine (PCA) for Pyroglutamic acid (UNK) for Unknown amino acid (ACE) for Acetylation cap (NH2) for Amidation cap (MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD Canonical sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides, corresponding to the sequence in attribute pdbx_seq_one_letter_code in category entity_poly. Non-standard amino acids/nucleotides are represented by the codes of their parents if parent is specified in attribute mon_nstd_parent_comp_id in category chem_comp, or by letter 'X' if parent is not specified. Deoxynucleotides are represented by their canonical one-letter codes of A, C, G, or T. MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD For cases in which the sample and model sequence differ this item contains the sample chemical sequence expressed as string of one-letter amino acid codes. Modified may be include as 'X' or with their 3-letter codes in parentheses. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other Chemical sequence expressed as string of three-letter amino acid codes. alanine ALA arginine ARG asparagine ASN aspartic-acid ASP ambiguous asparagine/aspartic-acid ASX cysteine CYS glutamine GLN glutamic-acid GLU glycine GLY ambiguous glutamine/glutamic acid GLX histidine HIS isoleucine ILE leucine LEU lysine LYS methionine MET phenylalanine PHE proline PRO serine SER threonine THR tryptophan TRP tyrosine TYR valine VAL 1-methyladenosine 1MA 5-methycytosine 5MC 2(prime)-O-methycytodine OMC 1-methyguanosine 1MG N(2)-methyguanosine 2MG N(2)-dimethyguanosine M2G 7-methyguanosine 7MG 2(prime)-O-methyguanosine 0MG diydrouridine H2U ribosylthymidine 5MU pseudouridine PSU acetic acid ACE formic acid FOR water HOH other UNK Evidence for the assignment of the polymer sequence. The PDB strand/chain id(s) corresponding to this polymer entity. A B A,B,C For Structural Genomics entries, the sequence's target identifier registered at the TargetTrack database. 356560 The type of the polymer. A description of special aspects of the polymer type. monomer Ala 16 is a D-amino acid the oligomer contains alternating RNA and DNA units This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_poly_seqCategory> <PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="1"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="2"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="3"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="4"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="5"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="TRP" num="6"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="7"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ARG" num="8"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="PRO" num="9"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="10"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="VAL" num="11"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="THR" num="12"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="13"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="14"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ILE" num="15"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="16"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLY" num="17"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLN" num="18"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="19"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LYS" num="20"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="GLU" num="21"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ALA" num="22"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="23"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="LEU" num="24"></PDBx:entity_poly_seq> <PDBx:entity_poly_seq entity_id="1" mon_id="ASP" num="25"></PDBx:entity_poly_seq> </PDBx:entity_poly_seqCategory> A flag to indicate whether this monomer in the polymer is heterogeneous in sequence. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The value of attribute num in category entity_poly_seq must uniquely and sequentially identify a record in the ENTITY_POLY_SEQ list. Note that this item must be a number and that the sequence numbers must progress in increasing numerical order. Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid). Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_src_genCategory> <PDBx:entity_src_gen entity_id="1" pdbx_src_id="1"> <PDBx:gene_src_common_name>HIV-1</PDBx:gene_src_common_name> <PDBx:gene_src_strain>NY-5</PDBx:gene_src_strain> <PDBx:host_org_common_name>bacteria</PDBx:host_org_common_name> <PDBx:host_org_genus>Escherichia</PDBx:host_org_genus> <PDBx:host_org_species>coli</PDBx:host_org_species> <PDBx:plasmid_name>pB322</PDBx:plasmid_name> </PDBx:entity_src_gen> </PDBx:entity_src_genCategory> A unique identifier for the expression system. This should be extracted from a local list of expression systems. The common name of the natural organism from which the gene was obtained. man yeast bacteria A description of special aspects of the natural organism from which the gene was obtained. A string to indicate the life-cycle or cell development cycle in which the gene is expressed and the mature protein is active. The genus of the natural organism from which the gene was obtained. Homo Saccharomyces Escherichia The species of the natural organism from which the gene was obtained. sapiens cerevisiae coli The strain of the natural organism from which the gene was obtained, if relevant. DH5a BMH 71-18 The tissue of the natural organism from which the gene was obtained. heart liver eye lens The subcellular fraction of the tissue of the natural organism from which the gene was obtained. mitochondria nucleus membrane The common name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item be derived from attribute host_org_common_name in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express yeast bacteria A description of special aspects of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would derived from attribute host_org_details in category entity_src_gen_express The genus of the organism that served as host for the production of the entity. Saccharomyces Escherichia The species of the organism that served as host for the production of the entity. cerevisiae coli The strain of the organism in which the entity was expressed. Where full details of the protein production are available it would be expected that this item be derived from attribute host_org_strain in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express DH5a BMH 71-18 This data item identifies cases in which an alternative source modeled. The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. Information on the source which is not given elsewhere. The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. American Type Culture Collection tissue culture number. 6051 Cell type. ENDOTHELIAL The specific line of cells. HELA CELLS Identifies the location inside (or outside) the cell. CYTOPLASM NUCLEUS Culture collection identifier. 6051 A domain or fragment of the molecule. CYTOPLASM NUCLEUS Identifies the gene. NCBI Taxonomy identifier for the gene source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. Organized group of tissues that carries on a specialized function. KIDNEY LIVER PANCREAS Organized structure within cell. MITOCHONDRIA The source plasmid. The source plasmid. Scientific name of the organism. ESCHERICHIA COLI HOMO SAPIENS SACCHAROMYCES CEREVISIAE Identifies the variant. DELTAH1DELTATRP Americal Tissue Culture Collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_culture_collection in category entity_src_gen_express Cell type from which the gene is derived. Where entity.target_id is provided this should be derived from details of the target. ENDOTHELIAL A specific line of cells used as the expression system. Where full details of the protein production are available it would be expected that this item would be derived from entity_src_gen_express.host_org_cell_line HELA Identifies the location inside (or outside) the cell which expressed the molecule. CYTOPLASM NUCLEUS Culture collection of the expression system. Where full details of the protein production are available it would be expected that this item would be derived somehwere, but exactly where is not clear. Specific gene which expressed the molecule. HIV-1 POL GLNS7 U1A (2-98, Y31H, Q36R) NCBI Taxonomy identifier for the expression system organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. Specific organ which expressed the molecule. KIDNEY Specific organelle which expressed the molecule. MITOCHONDRIA The scientific name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_scientific_name in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express ESCHERICHIA COLI SACCHAROMYCES CEREVISIAE The strain of the organism in which the entity was expressed. AR120 The specific tissue which expressed the molecule. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_tissue in category entity_src_gen_express heart liver eye lens The fraction of the tissue which expressed the molecule. mitochondria nucleus membrane Variant of the organism used as the expression system. Where full details of the protein production are available it would be expected that this item be derived from entity_src_gen_express.host_org_variant or via attribute host_org_tax_id in category entity_src_gen_express TRP-LAC LAMBDA DE3 Identifies the vector used. Where full details of the protein production are available it would be expected that this item would be derived from attribute vector_name in category entity_src_gen_clone. PBIT36 PET15B PUC18 Identifies the type of vector used (plasmid, virus, or cosmid). Where full details of the protein production are available it would be expected that this item would be derived from attribute vector_type in category entity_src_gen_express. COSMID PLASMID This data item povides additional information about the sequence type. A description of special aspects of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from attribute details in category pdbx_construct of the construct pointed to from attribute plasmid_id in category entity_src_gen_express. The name of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from attribute name in category pdbx_construct of the construct pointed to from attribute plasmid_id in category entity_src_gen_express. pET3C pT123sab A pointer to attribute id in category pdbx_construct in the PDBX_CONSTRUCT category. The indentified sequence is the initial construct. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is an ordinal identifier for entity_src_gen data records. Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entity_src_natCategory> <PDBx:entity_src_nat entity_id="2" pdbx_src_id="1"> <PDBx:common_name>bacteria</PDBx:common_name> <PDBx:details> Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka Prefecture University, and provided to us by Dr. Ben Dunn, University of Florida, and Dr. J. Kay, University of Wales.</PDBx:details> <PDBx:genus>Actinomycetes</PDBx:genus> </PDBx:entity_src_nat> </PDBx:entity_src_natCategory> The common name of the organism from which the entity was isolated. man yeast bacteria A description of special aspects of the organism from which the entity was isolated. The genus of the organism from which the entity was isolated. Homo Saccharomyces Escherichia This data item identifies cases in which an alternative source modeled. Americal Tissue Culture Collection number. 6051 The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. A particular cell type. BHK-21 The specific line of cells. HELA Identifies the location inside (or outside) the cell. Culture Collection identifier. 6051 The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. A domain or fragment of the molecule. NCBI Taxonomy identifier for the source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. Organized group of tissues that carries on a specialized function. KIDNEY Organized structure within cell. MITOCHONDRIA Scientific name of the organism of the natural source. BOS TAURUS SUS SCROFA ASPERGILLUS ORYZAE Details about the plasmid. PLC28 DERIVATIVE The plasmid containing the gene. pB322 Identifies the secretion from which the molecule was isolated. saliva urine venom Identifies the variant. The species of the organism from which the entity was isolated. sapiens cerevisiae coli The strain of the organism from which the entity was isolated. DH5a BMH 71-18 The tissue of the organism from which the entity was isolated. heart liver eye lens The subcellular fraction of the tissue of the organism from which the entity was isolated. mitochondria nucleus membrane This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is an ordinal identifier for entity_src_nat data records. There is only one item in the ENTRY category, attribute id in category entry. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:entryCategory> <PDBx:entry id="5HVP"></PDBx:entry> </PDBx:entryCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:entryCategory> <PDBx:entry id="TOZ"></PDBx:entry> </PDBx:entryCategory> Document Object Identifier (DOI) for this entry registered with http://crossref.org. The value of attribute id in category entry identifies the data block. Note that this item need not be a number; it can be any unique identifier. Data items in the ENTRY_LINK category record the relationships between the current data block identified by attribute id in category entry and other data blocks within the current file which may be referenced in the current data block. Example 1 - example file for the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <PDBx:entry_linkCategory> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_COM"> <PDBx:details>experimental data common to ref./mod. structures</PDBx:details> </PDBx:entry_link> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_REF"> <PDBx:details>reference structure</PDBx:details> </PDBx:entry_link> <PDBx:entry_link entry_id="KSE_TEXT" id="KSE_MOD"> <PDBx:details>modulated structure</PDBx:details> </PDBx:entry_link> </PDBx:entry_linkCategory> A description of the relationship between the data blocks identified by _entry_link.id and _entry_link.entry_id. This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category entry_link identifies a data block related to the current data block. Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <PDBx:exptlCategory> <PDBx:exptl entry_id="datablock1" method="single-crystal x-ray diffraction"> <PDBx:absorpt_coefficient_mu>1.22</PDBx:absorpt_coefficient_mu> <PDBx:absorpt_correction_T_max>0.896</PDBx:absorpt_correction_T_max> <PDBx:absorpt_correction_T_min>0.802</PDBx:absorpt_correction_T_min> <PDBx:absorpt_correction_type>integration</PDBx:absorpt_correction_type> <PDBx:absorpt_process_details> Gaussian grid method from SHELX76 Sheldrick, G. M., &quot;SHELX-76: structure determination and refinement program&quot;, Cambridge University, UK, 1976</PDBx:absorpt_process_details> <PDBx:crystals_number>1</PDBx:crystals_number> <PDBx:details> Enraf-Nonius LT2 liquid nitrogen variable-temperature device used</PDBx:details> <PDBx:method_details> graphite monochromatized Cu K(alpha) fixed tube and Enraf-Nonius CAD4 diffractometer used</PDBx:method_details> </PDBx:exptl> </PDBx:exptlCategory> The absorption coefficient mu in reciprocal millimetres calculated from the atomic content of the cell, the density and the radiation wavelength. The maximum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. The minimum transmission factor for the crystal and radiation. The maximum and minimum transmission factors are also referred to as the absorption correction A or 1/A*. The absorption correction type and method. The value 'empirical' should NOT be used unless more detailed information is not available. Description of the absorption process applied to the intensities. A literature reference should be supplied for psi-scan techniques. Tompa analytical The total number of crystals used in the measurement of intensities. Any special information about the experimental work prior to the intensity measurement. See also attribute preparation in category exptl_crystal. A description of special aspects of the experimental method. 29 structures minimized average structure This data item is a pointer to attribute id in category entry in the ENTRY category. The method used in the experiment. X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING POWDER DIFFRACTION Data items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:F_000>202</PDBx:F_000> <PDBx:colour>pale yellow</PDBx:colour> <PDBx:density_Matthews>1.01</PDBx:density_Matthews> <PDBx:density_diffrn>1.113</PDBx:density_diffrn> <PDBx:density_meas>1.11</PDBx:density_meas> <PDBx:density_meas_temp>294.5</PDBx:density_meas_temp> <PDBx:density_method>neutral buoyancy</PDBx:density_method> <PDBx:density_percent_sol>0.15</PDBx:density_percent_sol> <PDBx:description>hexagonal rod, uncut</PDBx:description> <PDBx:preparation> hanging drop, crystal soaked in 10&#37; ethylene glycol for 10 h, then placed in nylon loop at data collection time</PDBx:preparation> <PDBx:size_max>0.30</PDBx:size_max> <PDBx:size_mid>0.20</PDBx:size_mid> <PDBx:size_min>0.05</PDBx:size_min> <PDBx:size_rad>0.025</PDBx:size_rad> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> Example 2 - using separate items to define upper and lower limits for a value. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:density_meas_gt>2.5</PDBx:density_meas_gt> <PDBx:density_meas_lt>5.0</PDBx:density_meas_lt> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> Example 3 - here the density was measured at some unspecified temperature below room temperature. <PDBx:exptl_crystalCategory> <PDBx:exptl_crystal id="xst2l"> <PDBx:density_meas_temp_lt>300</PDBx:density_meas_temp_lt> </PDBx:exptl_crystal> </PDBx:exptl_crystalCategory> The effective number of electrons in the crystal unit cell contributing to F(000). This may contain dispersion contributions and is calculated as F(000) = [ sum (f~r~^2^ + f~i~^2^) ]^1/2^ f~r~ = real part of the scattering factors at theta = 0 degree f~i~ = imaginary part of the scattering factors at theta = 0 degree the sum is taken over each atom in the unit cell The colour of the crystal. dark green The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. The enumeration list of standardized names developed for the International Centre for Diffraction Data. The colour of a crystal is given by the combination of attribute colour_modifier in category exptl_crystal with attribute colour_primary in category exptl_crystal, as in 'dark-green' or 'bluish-violet', if necessary combined with attribute colour_lustre in category exptl_crystal, as in 'metallic-green'. The density of the crystal, expressed as the ratio of the volume of the asymmetric unit to the molecular mass of a monomer of the structure, in units of angstroms^3^ per dalton. Ref: Matthews, B. W. (1968). J. Mol. Biol. 33, 491-497. Density values calculated from the crystal cell and contents. The units are megagrams per cubic metre (grams per cubic centimetre). Density values measured using standard chemical and physical methods. The units are megagrams per cubic metre (grams per cubic centimetre). The estimated standard deviation of attribute density_meas in category exptl_crystal. The value above which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which attribute density_meas in category exptl_crystal should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under attribute density_meas in category exptl_crystal. lower limit for the density (only the range within which the density lies was given in the original paper) 2.5 The value below which the density measured using standard chemical and physical methods lies. The units are megagrams per cubic metre (grams per cubic centimetre). _exptl_crystal.density_meas_gt and _exptl_crystal.density_meas_lt should not be used to report new experimental work, for which attribute density_meas in category exptl_crystal should be used. These items are intended for use in reporting information in existing databases and archives which would be misleading if reported under attribute density_meas in category exptl_crystal. specimen floats in water 1.0 upper limit for the density (only the range within which the density lies was given in the original paper) 5.0 Temperature in kelvins at which attribute density_meas in category exptl_crystal was determined. The estimated standard deviation of attribute density_meas_temp in category exptl_crystal. Temperature in kelvins above which attribute density_meas in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and attribute density_meas_temp_lt in category exptl_crystal should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under attribute density_meas_temp in category exptl_crystal. Temperature in kelvins below which attribute density_meas in category exptl_crystal was determined. attribute density_meas_temp_gt in category exptl_crystal and attribute density_meas_temp_lt in category exptl_crystal should not be used for reporting new work, for which the correct temperature of measurement should be given. These items are intended for use in reporting information stored in databases or archives which would be misleading if reported under attribute density_meas_temp in category exptl_crystal. The density was measured at some unspecified temperature below room temperature. 300 The method used to measure attribute density_meas in category exptl_crystal. Density value P calculated from the crystal cell and contents, expressed as per cent solvent. P = 1 - (1.23 N MMass) / V N = the number of molecules in the unit cell MMass = the molecular mass of each molecule (gm/mole) V = the volume of the unit cell (A^3^) 1.23 = a conversion factor evaluated as: (0.74 cm^3^/g) (10^24^ A^3^/cm^3^) -------------------------------------- (6.02*10^23^) molecules/mole where 0.74 is an assumed value for the partial specific volume of the molecule A description of the quality and habit of the crystal. The crystal dimensions should not normally be reported here; use instead the specific items in the EXPTL_CRYSTAL category relating to size for the gross dimensions of the crystal and data items in the EXPTL_CRYSTAL_FACE category to describe the relationship between individual faces. The measured diffraction limit for this crystal. The measured diffraction limit for this crystal. The crystal size along the first measured direction in millimeters. The crystal size along the second measured direction in millimeters. The crystal size along the third measured direction in millimeters. A code to indicate that a crystal image is available for this crystal. The image format for the file containing the image of crystal specified as an RFC2045/RFC2046 mime type. jpeg gif tiff The URL for an a file containing the image of crystal. The of the distribution of mis-orientation angles specified in degrees of all the unit cells in the crystal. Lower mosaicity indicates better ordered crystals. The uncertainty in the mosaicity estimate for the crystal. A code to indicate that an x-ray image is available for this crystal. A description of the type of x-ray image for this crystal. Details of crystal growth and preparation of the crystal (e.g. mounting) prior to the intensity measurements. mounted in an argon-filled quartz capillary The maximum dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. The medial dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. The minimum dimension of the crystal. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. The radius of the crystal, if the crystal is a sphere or a cylinder. This item may appear in a list with attribute id in category exptl_crystal if multiple crystals are used in the experiment. The value of attribute id in category exptl_crystal must uniquely identify a record in the EXPTL_CRYSTAL list. Note that this item need not be a number; it can be any unique identifier. Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces. Example 1 - based on laboratory records for Yb(S-C5H4N)2(THF)4 for the 100 face of crystal xstl1. <PDBx:exptl_crystal_faceCategory> <PDBx:exptl_crystal_face crystal_id="xstl1" index_h="1" index_k="0" index_l="0"> <PDBx:diffr_chi>42.56</PDBx:diffr_chi> <PDBx:diffr_kappa>30.23</PDBx:diffr_kappa> <PDBx:diffr_phi>-125.56</PDBx:diffr_phi> <PDBx:diffr_psi>-0.34</PDBx:diffr_psi> <PDBx:perp_dist>0.025</PDBx:perp_dist> </PDBx:exptl_crystal_face> </PDBx:exptl_crystal_faceCategory> The chi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. The kappa diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. The phi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. The psi diffractometer setting angle in degrees for a specific crystal face associated with attribute perp_dist in category exptl_crystal_face. The perpendicular distance in millimetres from the face to the centre of rotation of the crystal. This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. Miller index h of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. Miller index k of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. Miller index l of the crystal face associated with the value attribute perp_dist in category exptl_crystal_face. Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:exptl_crystal_growCategory> <PDBx:exptl_crystal_grow crystal_id="1"> <PDBx:apparatus>Linbro plates</PDBx:apparatus> <PDBx:atmosphere>room air</PDBx:atmosphere> <PDBx:method>VAPOR DIFFUSION, HANGING DROP</PDBx:method> <PDBx:pH>4.7</PDBx:pH> <PDBx:temp>291</PDBx:temp> <PDBx:time>approximately 2 days</PDBx:time> </PDBx:exptl_crystal_grow> </PDBx:exptl_crystal_growCategory> The physical apparatus in which the crystal was grown. Linbro plate sandwich box ACA plates The nature of the gas or gas mixture in which the crystal was grown. room air nitrogen argon A description of special aspects of the crystal growth. Solution 2 was prepared as a well solution and mixed. A droplet containing 2 \ml of solution 1 was delivered onto a cover slip; 2 \ml of solution 2 was added to the droplet without mixing. Crystal plates were originally stored at room temperature for 1 week but no nucleation occurred. They were then transferred to 4 degrees C, at which temperature well formed single crystals grew in 2 days. The dependence on pH for successful crystal growth is very sharp. At pH 7.4 only showers of tiny crystals grew, at pH 7.5 well formed single crystals grew, at pH 7.6 no crystallization occurred at all. The method used to grow the crystals. MICROBATCH VAPOR DIFFUSION, HANGING DROP A literature reference that describes the method used to grow the crystals. McPherson et al., 1988 The pH at which the crystal was grown. If more than one pH was employed during the crystallization process, the final pH should be noted here and the protocol involving multiple pH values should be described in attribute details in category exptl_crystal_grow. 7.4 7.6 4.3 Text description of crystal growth procedure. PEG 4000, potassium phosphate, magnesium chloride, cacodylate The range of pH values at which the crystal was grown. Used when a point estimate of pH is not appropriate. 5.6 - 6.4 The ambient pressure in kilopascals at which the crystal was grown. The standard uncertainty (estimated standard deviation) of attribute pressure in category exptl_crystal_grow. A description of the protocol used for seeding the crystal growth. macroseeding Microcrystals were introduced from a previous crystal growth experiment by transfer with a human hair. A literature reference that describes the protocol used to seed the crystal. Stura et al., 1989 The temperature in kelvins at which the crystal was grown. If more than one temperature was employed during the crystallization process, the final temperature should be noted here and the protocol involving multiple temperatures should be described in attribute details in category exptl_crystal_grow. A description of special aspects of temperature control during crystal growth. The standard uncertainty (estimated standard deviation) of attribute temp in category exptl_crystal_grow. The approximate time that the crystal took to grow to the size used for data collection. overnight 2-4 days 6 months This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be given in attribute details in category exptl_crystal_grow_comp using the solutions described in EXPTL_CRYSTAL_GROW_COMP. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:exptl_crystal_grow_compCategory> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="1"> <PDBx:conc>6 mg/ml</PDBx:conc> <PDBx:details> The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/ MES buffer, pH 7.5, 3 mM NaAzide</PDBx:details> <PDBx:name>HIV-1 protease</PDBx:name> <PDBx:sol_id>1</PDBx:sol_id> <PDBx:volume>0.002 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="2"> <PDBx:conc>4 M</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>NaCl</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.200 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="3"> <PDBx:conc>100 mM</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.047 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="4"> <PDBx:conc>100 mM</PDBx:conc> <PDBx:details> in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured.</PDBx:details> <PDBx:name>Na Acetate</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.053 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> <PDBx:exptl_crystal_grow_comp crystal_id="1" id="5"> <PDBx:conc>neat</PDBx:conc> <PDBx:details>in 3 mM NaAzide</PDBx:details> <PDBx:name>water</PDBx:name> <PDBx:sol_id>2</PDBx:sol_id> <PDBx:volume>0.700 ml</PDBx:volume> </PDBx:exptl_crystal_grow_comp> </PDBx:exptl_crystal_grow_compCategory> The concentration of the solution component. 200 \ml 0.1 ml A description of any special aspects of the solution component. When the solution component is the one that contains the macromolecule, this could be the specification of the buffer in which the macromolecule was stored. When the solution component is a buffer component, this could be the methods (or formula) used to achieve a desired pH. in 3 mM NaAzide The protein solution was in a buffer containing 25 mM NaCl, 100 mM NaMES/MES buffer, pH 7.5, 3 mM NaAzide in 3 mM NaAzide. Buffer components were mixed to produce a pH of 4.7 according to a ratio calculated from the pKa. The actual pH of solution 2 was not measured. A common name for the component of the solution. protein in buffer acetic acid The identification of the cystallization bath. The concentration of this component in the final crystallization solution. This data item should include units of concentration. The identification of the crystallization salt. The identification of the crystallization soaking salt. The identification of the crystallization soaking solvent The identification of the crystallization solvent. An identifier for the solution to which the given solution component belongs. 1 well solution solution A The volume of the solution component. 200 \ml 0.1 ml This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. The value of attribute id in category exptl_crystal_grow_comp must uniquely identify each item in the EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. 1 A protein in buffer Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag. A description of geometry not covered by the existing data names in the GEOM categories, such as least-squares planes. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:geom_angleCategory> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="O1" atom_site_id_3="C5" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>111.6</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="C3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>110.9</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="O1" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>122.2</PDBx:value> <PDBx:value_esd>0.3</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C3" atom_site_id_2="C2" atom_site_id_3="O21" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>127.0</PDBx:value> <PDBx:value_esd>0.3</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="N4" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>101.3</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>111.3</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="C2" atom_site_id_2="C3" atom_site_id_3="H3" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>no</PDBx:publ_flag> <PDBx:value>107</PDBx:value> <PDBx:value_esd>1</PDBx:value_esd> </PDBx:geom_angle> <PDBx:geom_angle atom_site_id_1="N4" atom_site_id_2="C3" atom_site_id_3="C31" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>116.7</PDBx:value> <PDBx:value_esd>0.2</PDBx:value_esd> </PDBx:geom_angle> </PDBx:geom_angleCategory> An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. This code signals whether the angle is referred to in a publication or should be placed in a table of significant angles. Angle in degrees defined by the three sites _geom_angle.atom_site_id_1, _geom_angle.atom_site_id_2 and attribute atom_site_id_3 in category geom_angle. The standard uncertainty (estimated standard deviation) of attribute value in category geom_angle. The identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the three atom sites that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the third of the three atom sites that define the angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:geom_bondCategory> <PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C2" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.342</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="O1" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.439</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="C3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.512</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C2" atom_site_id_2="O21" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.199</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="N4" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.465</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="C31" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.537</PDBx:dist> <PDBx:dist_esd>0.004</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="C3" atom_site_id_2="H3" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.00</PDBx:dist> <PDBx:dist_esd>0.03</PDBx:dist_esd> <PDBx:publ_flag>no</PDBx:publ_flag> </PDBx:geom_bond> <PDBx:geom_bond atom_site_id_1="N4" atom_site_id_2="C5" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.472</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_bond> </PDBx:geom_bondCategory> An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The intramolecular bond distance in angstroms. The standard uncertainty (estimated standard deviation) of attribute dist in category geom_bond. Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. This code signals whether the bond distance is referred to in a publication or should be placed in a list of significant bond distances. The bond valence calculated from attribute dist in category geom_bond. The identifier of the first of the two atom sites that define the bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the two atom sites that define the bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the two atom sites that define the bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the two atom sites that define the bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. <PDBx:geom_contactCategory> <PDBx:geom_contact atom_site_id_1="O(1)" atom_site_id_2="O(2)" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>2.735</PDBx:dist> <PDBx:dist_esd>0.003</PDBx:dist_esd> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_contact> <PDBx:geom_contact atom_site_id_1="H(O1)" atom_site_id_2="O(2)" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>1.82</PDBx:dist> <PDBx:dist_esd xsi:nil="true" /> <PDBx:publ_flag>no</PDBx:publ_flag> </PDBx:geom_contact> </PDBx:geom_contactCategory> An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The interatomic contact distance in angstroms. The standard uncertainty (estimated standard deviation) of attribute dist in category geom_contact. Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. This code signals whether the contact distance is referred to in a publication or should be placed in a list of significant contact distances. The identifier of the first of the two atom sites that define the contact. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the two atom sites that define the contact. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the two atom sites that define the contact. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the two atom sites that define the contact. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data. Example 1 - based on C~14~H~13~ClN~2~O.H~2~O, reported by Palmer, Puddle & Lisgarten [Acta Cryst. (1993), C49, 1777-1779]. <PDBx:geom_hbondCategory> <PDBx:geom_hbond atom_site_id_A="OW" atom_site_id_D="N6" atom_site_id_H="HN6"> <PDBx:angle_DHA>169.6</PDBx:angle_DHA> <PDBx:dist_DA>2.801</PDBx:dist_DA> <PDBx:dist_DH>0.888</PDBx:dist_DH> <PDBx:dist_HA>1.921</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> <PDBx:geom_hbond atom_site_id_A="O7" atom_site_id_D="OW" atom_site_id_H="HO2"> <PDBx:angle_DHA>153.5</PDBx:angle_DHA> <PDBx:dist_DA>2.793</PDBx:dist_DA> <PDBx:dist_DH>0.917</PDBx:dist_DH> <PDBx:dist_HA>1.923</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> <PDBx:geom_hbond atom_site_id_A="N10" atom_site_id_D="OW" atom_site_id_H="HO1"> <PDBx:angle_DHA>179.7</PDBx:angle_DHA> <PDBx:dist_DA>2.842</PDBx:dist_DA> <PDBx:dist_DH>0.894</PDBx:dist_DH> <PDBx:dist_HA>1.886</PDBx:dist_HA> <PDBx:publ_flag>yes</PDBx:publ_flag> </PDBx:geom_hbond> </PDBx:geom_hbondCategory> The angle in degrees defined by the donor-, hydrogen- and acceptor-atom sites in a hydrogen bond. The standard uncertainty (estimated standard deviation) of attribute angle_DHA in category geom_hbond. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The distance in angstroms between the donor- and acceptor-atom sites in a hydrogen bond. The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_DA in category geom_hbond. The distance in angstroms between the donor- and hydrogen-atom sites in a hydrogen bond. The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_DH in category geom_hbond. The distance in angstroms between the hydrogen- and acceptor- atom sites in a hydrogen bond. The standard uncertainty (estimated standard deviation) in angstroms of attribute dist_HA in category geom_hbond. This code signals whether the hydrogen-bond information is referred to in a publication or should be placed in a table of significant hydrogen-bond geometry. The identifier of the acceptor-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the donor-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the hydrogen-atom site that defines the hydrogen bond. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the acceptor-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the donor-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the hydrogen-atom site that defines the hydrogen bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. The vector direction attribute atom_site_id_2 in category geom_torsion to attribute atom_site_id_3 in category geom_torsion is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523. Example 1 - based on data set CLPHO6 of Ferguson, Ruhl, McKervey & Browne [Acta Cryst. (1992), C48, 2262-2264]. <PDBx:geom_torsionCategory> <PDBx:geom_torsion atom_site_id_1="C(9)" atom_site_id_2="O(2)" atom_site_id_3="C(7)" atom_site_id_4="C(2)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>71.8</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(7)" atom_site_id_2="O(2)" atom_site_id_3="C(9)" atom_site_id_4="C(10)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="2_666"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>-168.0</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(10)" atom_site_id_2="O(3)" atom_site_id_3="C(8)" atom_site_id_4="C(6)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>-167.7</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="C(8)" atom_site_id_2="O(3)" atom_site_id_3="C(10)" atom_site_id_4="C(9)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="2_666"> <PDBx:publ_flag>yes</PDBx:publ_flag> <PDBx:value>-69.7</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(3)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:publ_flag>no</PDBx:publ_flag> <PDBx:value>-179.5</PDBx:value> </PDBx:geom_torsion> <PDBx:geom_torsion atom_site_id_1="O(1)" atom_site_id_2="C(1)" atom_site_id_3="C(2)" atom_site_id_4="C(7)" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:publ_flag>no</PDBx:publ_flag> <PDBx:value>-0.6</PDBx:value> </PDBx:geom_torsion> </PDBx:geom_torsionCategory> An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. This code signals whether the torsion angle is referred to in a publication or should be placed in a table of significant torsion angles. The value of the torsion angle in degrees. The standard uncertainty (estimated standard deviation) of attribute value in category geom_torsion. The identifier of the first of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the third of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the fourth of the four atom sites that define the torsion angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The symmetry code of the first of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the third of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the fourth of the four atom sites that define the torsion angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication. The creator of a data block will not normally specify these data. The data names are not defined in the dictionary because they are for journal use only. Example 1 - based on Acta Cryst. file for entry HL0007 [Willis, Beckwith & Tozer (1991). Acta Cryst. C47, 2276-2277]. <PDBx:journalCategory> <PDBx:journal entry_id="TOZ"> <PDBx:coden_ASTM>ACSCEE</PDBx:coden_ASTM> <PDBx:coeditor_code>HL0007</PDBx:coeditor_code> <PDBx:date_accepted>1991-04-18</PDBx:date_accepted> <PDBx:date_from_coeditor>1991-04-18</PDBx:date_from_coeditor> <PDBx:date_printers_first>1991-08-07</PDBx:date_printers_first> <PDBx:date_proofs_out>1991-08-07</PDBx:date_proofs_out> <PDBx:date_recd_electronic>1991-04-15</PDBx:date_recd_electronic> <PDBx:issue>NOV91</PDBx:issue> <PDBx:name_full>Acta Crystallographica Section C</PDBx:name_full> <PDBx:page_first>2276</PDBx:page_first> <PDBx:page_last>2277</PDBx:page_last> <PDBx:techeditor_code>C910963</PDBx:techeditor_code> <PDBx:volume>47</PDBx:volume> <PDBx:year>1991</PDBx:year> </PDBx:journal> </PDBx:journalCategory> Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. Journal data items are defined by the journal staff. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a data block will not normally specify these data items. Example 1 - based on a paper by Zhu, Reynolds, Klein & Trudell [Acta Cryst. (1994), C50, 2067-2069]. <PDBx:journal_indexCategory> <PDBx:journal_index term="C16H19NO4" type="O"> <PDBx:subterm xsi:nil="true" /> </PDBx:journal_index> <PDBx:journal_index term="alkaloids" type="S"> <PDBx:subterm>(-)-norcocaine</PDBx:subterm> </PDBx:journal_index> <PDBx:journal_index term="(-)-norcocaine" type="S"> <PDBx:subterm xsi:nil="true" /> </PDBx:journal_index> <PDBx:journal_index term=" [2R,3S-(2\b,3\b)]-methyl 3-(benzoyloxy)-8-azabicyclo[3.2.1]octane-2-carboxylate" type="S"> <PDBx:subterm xsi:nil="true" /> </PDBx:journal_index> </PDBx:journal_indexCategory> Journal index data items are defined by the journal staff. Journal index data items are defined by the journal staff. Journal index data items are defined by the journal staff. Placeholder category for PDB coordinate data. Placeholder item to hold unparsed coordinate data. Data items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry. This data item counts the number of occurences of this feature in this entry. This data item is a pointer to attribute id in category entry in the ENTRY category. This data item identifies a secondary structure feature of this entry. Data items in the NDB_STRUCT_FEATURE_NA category describes tertiary and other special structural features in this entry. This data item counts the number of occurences of this feature in this entry. This data item is a pointer to attribute id in category entry in the ENTRY category. This data item identifies a structural feature of this entry. Data items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions. <PDBx:ndb_struct_na_base_pairCategory> <PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="1" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="8" j_symmetry="7_555" model_number="1"> <PDBx:buckle>-5.523</PDBx:buckle> <PDBx:opening>-3.291</PDBx:opening> <PDBx:propeller>-6.752</PDBx:propeller> <PDBx:shear>-0.396</PDBx:shear> <PDBx:stagger>-0.018</PDBx:stagger> <PDBx:stretch>-0.156</PDBx:stretch> </PDBx:ndb_struct_na_base_pair> <PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="2" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="7" j_symmetry="7_555" model_number="1"> <PDBx:buckle>-4.727</PDBx:buckle> <PDBx:opening>2.311</PDBx:opening> <PDBx:propeller>-9.765</PDBx:propeller> <PDBx:shear>-0.094</PDBx:shear> <PDBx:stagger>-0.334</PDBx:stagger> <PDBx:stretch>-0.220</PDBx:stretch> </PDBx:ndb_struct_na_base_pair> <PDBx:ndb_struct_na_base_pair i_label_asym_id="A" i_label_comp_id="G" i_label_seq_id="3" i_symmetry="1_555" j_label_asym_id="A" j_label_comp_id="C" j_label_seq_id="6" j_symmetry="7_555" model_number="1"> <PDBx:buckle>-6.454</PDBx:buckle> <PDBx:opening>-1.181</PDBx:opening> <PDBx:propeller>-12.575</PDBx:propeller> <PDBx:shear>-0.285</PDBx:shear> <PDBx:stagger>0.008</PDBx:stagger> <PDBx:stretch>-0.239</PDBx:stretch> </PDBx:ndb_struct_na_base_pair> </PDBx:ndb_struct_na_base_pairCategory> The value of the base pair buckle parameter. Base pair classification of Westhoff and Leontis. Base pair classification of Saenger Describes the PDB insertion code of the i-th base in the base pair. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the asym id of the i-th base in the base pair. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the i-th base in the base pair. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Describes the PDB insertion code of the j-th base in the base pair. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the asym id of the j-th base in the base pair. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the j-th base in the base pair. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the base pair opening parameter. Text label for this base pair. Sequential number of pair in the pair sequence. The value of the base pair propeller parameter. The value of the base pair shear parameter. The value of the base pair stagger parameter. The value of the base pair stretch parameter. Describes the asym id of the i-th base in the base pair. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the component id of the i-th base in the base pair. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the i-th base in the base pair. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the base pair. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the asym id of the j-th base in the base pair. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the component id of the j-th base in the base pair. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the j-th base in the base pair. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the base pair. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the model number of the base pair. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions. <PDBx:ndb_struct_na_base_pair_stepCategory> <PDBx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="1" i_label_seq_id_2="2" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="8" j_label_seq_id_2="7" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1"> <PDBx:rise>3.339</PDBx:rise> <PDBx:roll>9.755</PDBx:roll> <PDBx:shift>0.369</PDBx:shift> <PDBx:slide>-1.414</PDBx:slide> <PDBx:tilt>3.056</PDBx:tilt> <PDBx:twist>33.530</PDBx:twist> </PDBx:ndb_struct_na_base_pair_step> <PDBx:ndb_struct_na_base_pair_step i_label_asym_id_1="A" i_label_asym_id_2="A" i_label_comp_id_1="G" i_label_comp_id_2="G" i_label_seq_id_1="2" i_label_seq_id_2="3" i_symmetry_1="1_555" i_symmetry_2="1_555" j_label_asym_id_1="A" j_label_asym_id_2="A" j_label_comp_id_1="C" j_label_comp_id_2="C" j_label_seq_id_1="7" j_label_seq_id_2="6" j_symmetry_1="7_555" j_symmetry_2="7_555" model_number="1"> <PDBx:rise>3.371</PDBx:rise> <PDBx:roll>6.725</PDBx:roll> <PDBx:shift>0.176</PDBx:shift> <PDBx:slide>-1.672</PDBx:slide> <PDBx:tilt>-1.176</PDBx:tilt> <PDBx:twist>30.004</PDBx:twist> </PDBx:ndb_struct_na_base_pair_step> </PDBx:ndb_struct_na_base_pair_stepCategory> The value of the base pair step helical rise parameter. The value of the base pair step helical twist parameter. Describes the PDB insertion code of the i-th base in the first base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the PDB insertion code of the i-th base in the second base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the author's asym id of the i-th base in the first base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the author's asym id of the i-th base in the second base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the author's sequence number of the i-th base in the first base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Describes the author's sequence number of the i-th base in the second base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the base pair step inclination parameter. Describes the PDB insertion code of the j-th base in the first base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the PDB insertion code of the j-th base in the second base pair of the step. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Describes the author's asym id of the j-th base in the first base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the author's asym id of the j-th base in the second base pair of the step. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Describes the author's sequence number of the j-th base in the first base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Describes the author's sequence number of the j-th base in the second base pair of the step. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the base pair step rise parameter. The value of the base pair step roll parameter. The value of the base pair step shift parameter. The value of the base pair step slide parameter. The text name of this step. The sequence number of this step in the step sequence. The value of the base pair step tilt parameter. The value of the base pair step twist parameter. The value of the base pair step twist parameter. The value of the base pair step X displacement parameter. The value of the base pair step Y displacement parameter. Describes the asym id of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the asym id of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the component id of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the component id of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the i-th base in the first base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the i-th base in the second base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the first base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the symmetry operation that should be applied to the coordinates of the i-th base to generate the first partner in the second base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the asym id of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the asym id of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Describes the component id of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the component id of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the j-th base in the first base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the sequence number of the j-th base in the second base pair of the step. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the first base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the symmetry operation that should be applied to the coordinates of the j-th base to generate the second partner in the second base pair of the step. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Describes the model number of the base pair step. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Data items in the PDBX_CONTACT_AUTHOR category record details about the Structural Genomics Project and name and initials for each Center. Example 1 - <PDBx:pdbx_SG_projectCategory> <PDBx:pdbx_SG_project id="1"> <PDBx:full_name_of_center>Berkeley Structural Genomics Center</PDBx:full_name_of_center> <PDBx:initial_of_center>BSGC</PDBx:initial_of_center> <PDBx:project_name>PSI, Protein Structure Initiative</PDBx:project_name> </PDBx:pdbx_SG_project> </PDBx:pdbx_SG_projectCategory> The value identifies the full name of center. Midwest Center for Structural Genomics The value identifies the full name of center. JCSG The value identifies the Structural Genomics project. PSI, Protein Structure Initiative A unique integer identifier for this center 1 2 3 Gives information about the organization of the NDB Structural Atlas. Text of the Atlas index entry. Entry ID. A unique identifier for a NDB ATLAS index page. Data items in the PDBX_ATOM_SITE_ANISO_TLS category record details about the TLS contribution to anisotropic displacement parameters. Example 1 <PDBx:pdbx_atom_site_aniso_tlsCategory> <PDBx:pdbx_atom_site_aniso_tls id="1" tls_group_id="1"> <PDBx:U_tls11>2541</PDBx:U_tls11> <PDBx:U_tls12>676</PDBx:U_tls12> <PDBx:U_tls13>-827</PDBx:U_tls13> <PDBx:U_tls22>2835</PDBx:U_tls22> <PDBx:U_tls23>341</PDBx:U_tls23> <PDBx:U_tls33>3175</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>CB</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="2" tls_group_id="1"> <PDBx:U_tls11>3708</PDBx:U_tls11> <PDBx:U_tls12>633</PDBx:U_tls12> <PDBx:U_tls13>-724</PDBx:U_tls13> <PDBx:U_tls22>3876</PDBx:U_tls22> <PDBx:U_tls23>342</PDBx:U_tls23> <PDBx:U_tls33>4181</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>OG</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="3" tls_group_id="1"> <PDBx:U_tls11>7054</PDBx:U_tls11> <PDBx:U_tls12>619</PDBx:U_tls12> <PDBx:U_tls13>-966</PDBx:U_tls13> <PDBx:U_tls22>7457</PDBx:U_tls22> <PDBx:U_tls23>344</PDBx:U_tls23> <PDBx:U_tls33>7553</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>C</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="4" tls_group_id="1"> <PDBx:U_tls11>6837</PDBx:U_tls11> <PDBx:U_tls12>567</PDBx:U_tls12> <PDBx:U_tls13>-974</PDBx:U_tls13> <PDBx:U_tls22>7210</PDBx:U_tls22> <PDBx:U_tls23>341</PDBx:U_tls23> <PDBx:U_tls33>7184</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>O</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="5" tls_group_id="1"> <PDBx:U_tls11>5792</PDBx:U_tls11> <PDBx:U_tls12>538</PDBx:U_tls12> <PDBx:U_tls13>-778</PDBx:U_tls13> <PDBx:U_tls22>6180</PDBx:U_tls22> <PDBx:U_tls23>290</PDBx:U_tls23> <PDBx:U_tls33>6271</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>N</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>N</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> <PDBx:pdbx_atom_site_aniso_tls id="6" tls_group_id="1"> <PDBx:U_tls11>8440</PDBx:U_tls11> <PDBx:U_tls12>616</PDBx:U_tls12> <PDBx:U_tls13>-861</PDBx:U_tls13> <PDBx:U_tls22>8771</PDBx:U_tls22> <PDBx:U_tls23>331</PDBx:U_tls23> <PDBx:U_tls33>8935</PDBx:U_tls33> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>CA</PDBx:auth_atom_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_atom_site_aniso_tls> </PDBx:pdbx_atom_site_aniso_tlsCategory> This data item is a pointer to attribute pdbx_ins_code in category atom_site in the ATOM_SITE category. The [1][1] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. The [1][2] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. The [1][3] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. The [2][2] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. The [2][3] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. The [3][3] element of the TLS contribution to the atomic displacement matrix U. The unique elements of the real symmetric matrix are entered by row. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITE category. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. This data item identifies the TLS group membership for this atom. The PDBX_AUDIT holds current version information. The value of attribute entry_id in category pdbx_audit identifies the data block. 1 The value of attribute entry_id in category pdbx_audit identifies the data block. BDL001 Data items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP <PDBx:pdbx_audit_authorCategory> <PDBx:pdbx_audit_author ordinal="1"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Fitzgerald, Paula M.D.</PDBx:name> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="2"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>McKeever, Brian M.</PDBx:name> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="3"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Van Middlesworth, J.F.</PDBx:name> </PDBx:pdbx_audit_author> <PDBx:pdbx_audit_author ordinal="4"> <PDBx:address> Department of Biophysical Chemistry Merck Research Laboratories P. O. Box 2000, Ry80M203 Rahway, New Jersey 07065 USA</PDBx:address> <PDBx:name>Springer, James P.</PDBx:name> </PDBx:pdbx_audit_author> </PDBx:pdbx_audit_authorCategory> The address of an author of this data block. If there are multiple authors, attribute address in category pdbx_audit_author is looped with attribute name in category pdbx_audit_author. Department Institute Street City and postcode COUNTRY The name of an author of this data block. If there are multiple authors, _pdbx_audit_author.name is looped with _pdbx_audit_author.address. The family name(s), followed by a comma and including any dynastic compoents, precedes the first name(s) or initial(s). Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A A unique sequential integer identifier for each author. 1 2 3 Data items in the PDBX_AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant. Example 1 - Data file conforming to the current PDBx/mmCIF dictionary. <PDBx:pdbx_audit_conformCategory> <PDBx:pdbx_audit_conform dict_name="mmcif_pdbx.dic" dict_version="5.339"> <PDBx:dict_location>https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic</PDBx:dict_location> </PDBx:pdbx_audit_conform> </PDBx:pdbx_audit_conformCategory> A file name or uniform resource locator (URL) for the dictionary to which the current data block conforms. The dictionary name defining data names used in this file. The version number of the dictionary to which the current data block conforms. Data items in the PDBX_AUDIT_CONFORM_EXTENSION category describe extension dictionary versions against which the data names appearing the current data block are conformant. Example 1 - Conforming to EMD V 1.0 extension dictionary. <PDBx:pdbx_audit_conform_extensionCategory> <PDBx:pdbx_audit_conform_extension extension_dict_name="EMD" extension_dict_version="1.0"> <PDBx:extension_dict_location>http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v5_next.dic</PDBx:extension_dict_location> </PDBx:pdbx_audit_conform_extension> </PDBx:pdbx_audit_conform_extensionCategory> A file name or uniform resource locator (URL) for the file containing the extension dictionary. An identifier for the extension dictionary to which the current data block conforms. The version number of the extension dictionary to which the currrent data block conforms. Data items in the PDBX_AUDIT_REVISION_CATEGORY category report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 <PDBx:pdbx_audit_revision_categoryCategory> <PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <PDBx:category>audit_author</PDBx:category> </PDBx:pdbx_audit_revision_category> <PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="2" revision_ordinal="1"> <PDBx:category>citation</PDBx:category> </PDBx:pdbx_audit_revision_category> <PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="3" revision_ordinal="1"> <PDBx:category>citation_author</PDBx:category> </PDBx:pdbx_audit_revision_category> <PDBx:pdbx_audit_revision_category data_content_type="Structure model" ordinal="4" revision_ordinal="2"> <PDBx:category>citation</PDBx:category> </PDBx:pdbx_audit_revision_category> </PDBx:pdbx_audit_revision_categoryCategory> The category updated in the pdbx_audit_revision_category record. audit_author citation The type of file that the pdbx_audit_revision_history record refers to. Structure model A unique identifier for the pdbx_audit_revision_category record. 1 A pointer to attribute ordinal in category pdbx_audit_revision_history 1 Data items in the PDBX_audit_revision_details category record descriptions of changes associated with PDBX_AUDIT_REVISION_HISTORY records. Example 1 <PDBx:pdbx_audit_revision_detailsCategory> <PDBx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <PDBx:provider>repository</PDBx:provider> <PDBx:type>Initial release</PDBx:type> </PDBx:pdbx_audit_revision_details> <PDBx:pdbx_audit_revision_details data_content_type="Structure model" ordinal="2" revision_ordinal="7"> <PDBx:description>Remodeling of inhibitor</PDBx:description> <PDBx:provider>author</PDBx:provider> <PDBx:type>Coordinate replacement</PDBx:type> </PDBx:pdbx_audit_revision_details> </PDBx:pdbx_audit_revision_detailsCategory> Additional details describing the revision. Further details describing the revision. The provider of the revision. repository A type classification of the revision Initial release The type of file that the pdbx_audit_revision_history record refers to. Structure model A unique identifier for the pdbx_audit_revision_details record. 1 A pointer to attribute ordinal in category pdbx_audit_revision_history 1 Data items in the PDBX_AUDIT_revision_group category report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 <PDBx:pdbx_audit_revision_groupCategory> <PDBx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="1" revision_ordinal="2"> <PDBx:group>citation</PDBx:group> </PDBx:pdbx_audit_revision_group> <PDBx:pdbx_audit_revision_group data_content_type="Structure model" ordinal="2" revision_ordinal="3"> <PDBx:group>sample</PDBx:group> </PDBx:pdbx_audit_revision_group> </PDBx:pdbx_audit_revision_groupCategory> The collection of categories updated with this revision. citation The type of file that the pdbx_audit_revision_history record refers to. Structure model A unique identifier for the pdbx_audit_revision_group record. 1 A pointer to attribute ordinal in category pdbx_audit_revision_history 1 Data items in the PDBX_AUDIT_REVISION_HISTORY category record the revision history for a data entry. Example 1 <PDBx:pdbx_audit_revision_historyCategory> <PDBx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="1"> <PDBx:internal_deposition_id>D_123456789</PDBx:internal_deposition_id> <PDBx:internal_version>4</PDBx:internal_version> <PDBx:major_revision>1</PDBx:major_revision> <PDBx:minor_revision>0</PDBx:minor_revision> <PDBx:revision_date>2017-03-01</PDBx:revision_date> </PDBx:pdbx_audit_revision_history> <PDBx:pdbx_audit_revision_history data_content_type="Structure model" ordinal="2"> <PDBx:internal_deposition_id>D_123456789</PDBx:internal_deposition_id> <PDBx:internal_version>6</PDBx:internal_version> <PDBx:major_revision>1</PDBx:major_revision> <PDBx:minor_revision>1</PDBx:minor_revision> <PDBx:revision_date>2017-03-08</PDBx:revision_date> </PDBx:pdbx_audit_revision_history> </PDBx:pdbx_audit_revision_historyCategory> The deposition id that corresponds to this millestone file D_123456789 An internal version number corresponding to millestone file 13 The major version number of deposition release. 1 The minor version number of deposition release. 1 The release date of the revision 2017-03-08 The type of file that the pdbx_audit_revision_history record refers to. Structure model A unique identifier for the pdbx_audit_revision_history record. 1 Data items in the PDBX_AUDIT_REVISION_ITEM category report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record. Example 1 <PDBx:pdbx_audit_revision_itemCategory> <PDBx:pdbx_audit_revision_item data_content_type="Structure model" ordinal="1" revision_ordinal="1"> <PDBx:item>_atom_site.type_symbol</PDBx:item> </PDBx:pdbx_audit_revision_item> </PDBx:pdbx_audit_revision_itemCategory> A high level explanation the author has provided for submitting a revision. _atom_site.type_symbol The type of file that the pdbx_audit_revision_history record refers to. Structure model A unique identifier for the pdbx_audit_revision_item record. 1 A pointer to attribute ordinal in category pdbx_audit_revision_history 1 Data items in the PDBX_AUDIT_SUPPORT category record details about funding support for the entry. Example 1 - <PDBx:pdbx_audit_supportCategory> <PDBx:pdbx_audit_support ordinal="1"> <PDBx:country>United States</PDBx:country> <PDBx:funding_organization>National Institutes of Health/National Institute of General Medical Sciences</PDBx:funding_organization> <PDBx:grant_number>1R01GM072999-01</PDBx:grant_number> </PDBx:pdbx_audit_support> </PDBx:pdbx_audit_supportCategory> The country/region providing the funding support for the entry. Additional details regarding the funding of this entry The name of the organization providing funding support for the entry. National Institutes of Health Wellcome Trust National Institutes of Health/National Institute of General Medical Sciences The grant number associated with this source of support. A unique sequential integer identifier for each source of support for this entry. 1 2 3 This category provides a table of upper and lower distance limits used as criteria in determining covalent bonds. The table is organized by atom type pairs. Example 1 - Abbreviated bond distance limit table <PDBx:pdbx_bond_distance_limitsCategory> <PDBx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Ag"> <PDBx:lower_limit>1.85</PDBx:lower_limit> <PDBx:upper_limit>2.70</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Ag"> <PDBx:lower_limit>1.85</PDBx:lower_limit> <PDBx:upper_limit>2.70</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Ag"> <PDBx:lower_limit>2.00</PDBx:lower_limit> <PDBx:upper_limit>3.00</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="Al" atom_type_2="H"> <PDBx:lower_limit>1.35</PDBx:lower_limit> <PDBx:upper_limit>1.65</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="As" atom_type_2="H"> <PDBx:lower_limit>1.20</PDBx:lower_limit> <PDBx:upper_limit>1.60</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="N" atom_type_2="Au"> <PDBx:lower_limit>1.80</PDBx:lower_limit> <PDBx:upper_limit>2.80</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="O" atom_type_2="Au"> <PDBx:lower_limit>1.80</PDBx:lower_limit> <PDBx:upper_limit>2.80</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="S" atom_type_2="Au"> <PDBx:lower_limit>1.80</PDBx:lower_limit> <PDBx:upper_limit>3.00</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="B" atom_type_2="B"> <PDBx:lower_limit>1.45</PDBx:lower_limit> <PDBx:upper_limit>1.95</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="C" atom_type_2="B"> <PDBx:lower_limit>1.20</PDBx:lower_limit> <PDBx:upper_limit>1.85</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> <PDBx:pdbx_bond_distance_limits atom_type_1="F" atom_type_2="B"> <PDBx:lower_limit>1.20</PDBx:lower_limit> <PDBx:upper_limit>1.75</PDBx:upper_limit> </PDBx:pdbx_bond_distance_limits> </PDBx:pdbx_bond_distance_limitsCategory> The lower bond distance limit. The upper bond distance limit. The first atom type defining the bond C N P The first atom type defining the bond C N P The PDBX_BRANCH_SCHEME category provides residue level nomenclature mapping for branch chain entities. Example 1 - <PDBx:pdbx_branch_schemeCategory> <PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="NAG" num="1"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_mon_id>NAG</PDBx:auth_mon_id> <PDBx:auth_seq_num>1592</PDBx:auth_seq_num> <PDBx:hetero>n</PDBx:hetero> <PDBx:pdb_asym_id>B</PDBx:pdb_asym_id> <PDBx:pdb_mon_id>NAG</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>1</PDBx:pdb_seq_num> </PDBx:pdbx_branch_scheme> <PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="GAL" num="2"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_mon_id>GAL</PDBx:auth_mon_id> <PDBx:auth_seq_num>1591</PDBx:auth_seq_num> <PDBx:hetero>n</PDBx:hetero> <PDBx:pdb_asym_id>B</PDBx:pdb_asym_id> <PDBx:pdb_mon_id>GAL</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>2</PDBx:pdb_seq_num> </PDBx:pdbx_branch_scheme> <PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="3"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_mon_id>FUC</PDBx:auth_mon_id> <PDBx:auth_seq_num>1590</PDBx:auth_seq_num> <PDBx:hetero>n</PDBx:hetero> <PDBx:pdb_asym_id>B</PDBx:pdb_asym_id> <PDBx:pdb_mon_id>FUC</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>3</PDBx:pdb_seq_num> </PDBx:pdbx_branch_scheme> <PDBx:pdbx_branch_scheme asym_id="B" entity_id="2" mon_id="FUC" num="4"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_mon_id>FUC</PDBx:auth_mon_id> <PDBx:auth_seq_num>1593</PDBx:auth_seq_num> <PDBx:hetero>n</PDBx:hetero> <PDBx:pdb_asym_id>B</PDBx:pdb_asym_id> <PDBx:pdb_mon_id>FUC</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>4</PDBx:pdb_seq_num> </PDBx:pdbx_branch_scheme> </PDBx:pdbx_branch_schemeCategory> This data item is a pointer to attribute pdbx_auth_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute pdbx_auth_comp_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute pdbx_auth_seq_id in category atom_site in the ATOM_SITE category. A flag to indicate whether this monomer in the entity is heterogeneous in sequence. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute label_comp_id in category atom_site in the PDBX_ENTITY_BRANCH_LIST category. This data item is a pointer to attribute num in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. Data items in the PDBX_BUFFER category record details of the sample buffer. Any additional details to do with buffer. aerated The name of each buffer. Acetic acid The value of attribute id in category pdbx_buffer must uniquely identify the sample buffer. Constituents of buffer in sample Example 1 - based on PDB entry 1DYL and laboratory records for the structure corresponding to PDB entry 1DYL <PDBx:pdbx_buffer_componentsCategory> <PDBx:pdbx_buffer_components buffer_id="1" id="1"> <PDBx:conc>4 </PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>NaCl</PDBx:name> <PDBx:volume>0.200 </PDBx:volume> </PDBx:pdbx_buffer_components> <PDBx:pdbx_buffer_components buffer_id="1" id="2"> <PDBx:conc>100</PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>Acetic Acid</PDBx:name> <PDBx:volume>0.047 </PDBx:volume> </PDBx:pdbx_buffer_components> <PDBx:pdbx_buffer_components buffer_id="1" id="3"> <PDBx:conc>neat</PDBx:conc> <PDBx:details xsi:nil="true" /> <PDBx:name>water</PDBx:name> <PDBx:volume>0.700 </PDBx:volume> </PDBx:pdbx_buffer_components> </PDBx:pdbx_buffer_componentsCategory> The millimolar concentration of buffer component. 200 The concentration units of the component. mg/mL for mg per milliliter mM for millimolar % for percent by volume Any additional details to do with buffer composition. pH adjusted with NaOH The isotopic composition of each component, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labled biomolecule is designated by NA: U-13C; NA-K,H U-15N U-13C U-15N,13C U-2H other The name of each buffer component. Acetic acid The volume of buffer component. 0.200 This data item is a pointer to attribute id in category pdbx_buffer in the BUFFER category. The value of attribute id in category pdbx_buffer_components must uniquely identify a component of the buffer. Data items in the PDBX_CHEM_COMP_ATOM_EDIT category provide atom level editing instructions to be applied to imported chemical components. Example 1 - <PDBx:pdbx_chem_comp_atom_editCategory> <PDBx:pdbx_chem_comp_atom_edit ordinal="1"> <PDBx:atom_id>HN2</PDBx:atom_id> <PDBx:comp_id>LYS</PDBx:comp_id> <PDBx:edit_op>DELETE</PDBx:edit_op> </PDBx:pdbx_chem_comp_atom_edit> </PDBx:pdbx_chem_comp_atom_editCategory> The identifier for the target atom in imported component to be edited. This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP category. The identifier for the edited atom in the generated component. The value for the edited atomic property value in the generated component. The operation applied to the named imported component. This data item uniquely identifies and orders each atom edit instruction. Data items in the PDBX_CHEM_COMP_ATOM_FEATURE category provide a selected list of atom level features for the chemical component. Example 1 - <PDBx:pdbx_chem_comp_atom_featureCategory> <PDBx:pdbx_chem_comp_atom_feature atom_id="N" comp_id="LYS" feature_type="NT"></PDBx:pdbx_chem_comp_atom_feature> <PDBx:pdbx_chem_comp_atom_feature atom_id="C" comp_id="LYS" feature_type="CT"></PDBx:pdbx_chem_comp_atom_feature> <PDBx:pdbx_chem_comp_atom_feature atom_id="CA" comp_id="LYS" feature_type="CPA"></PDBx:pdbx_chem_comp_atom_feature> </PDBx:pdbx_chem_comp_atom_featureCategory> The identifier for the target atom to which the feature is assigned. This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP category. The feature assigned to this atom. PDBX_CHEM_COMP_ATOM_RELATED provides atom level nomenclature mapping between two related chemical components. Example 1 - <PDBx:pdbx_chem_comp_atom_relatedCategory> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="1" related_comp_id="GLC"> <PDBx:atom_id>C1</PDBx:atom_id> <PDBx:related_atom_id>C1</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="2" related_comp_id="GLC"> <PDBx:atom_id>C2</PDBx:atom_id> <PDBx:related_atom_id>C2</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="3" related_comp_id="GLC"> <PDBx:atom_id>C3</PDBx:atom_id> <PDBx:related_atom_id>C3</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="4" related_comp_id="GLC"> <PDBx:atom_id>C4</PDBx:atom_id> <PDBx:related_atom_id>C4</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="5" related_comp_id="GLC"> <PDBx:atom_id>C5</PDBx:atom_id> <PDBx:related_atom_id>C5</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="6" related_comp_id="GLC"> <PDBx:atom_id>C6</PDBx:atom_id> <PDBx:related_atom_id>C6</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="7" related_comp_id="GLC"> <PDBx:atom_id>N</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="8" related_comp_id="GLC"> <PDBx:atom_id>O1</PDBx:atom_id> <PDBx:related_atom_id>O1</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="9" related_comp_id="GLC"> <PDBx:atom_id>O3</PDBx:atom_id> <PDBx:related_atom_id>O3</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="10" related_comp_id="GLC"> <PDBx:atom_id>O4</PDBx:atom_id> <PDBx:related_atom_id>O4</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="11" related_comp_id="GLC"> <PDBx:atom_id>O5</PDBx:atom_id> <PDBx:related_atom_id>O5</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="12" related_comp_id="GLC"> <PDBx:atom_id>O6</PDBx:atom_id> <PDBx:related_atom_id>O6</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="13" related_comp_id="GLC"> <PDBx:atom_id>S1</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="14" related_comp_id="GLC"> <PDBx:atom_id>O1S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="15" related_comp_id="GLC"> <PDBx:atom_id>O2S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="16" related_comp_id="GLC"> <PDBx:atom_id>O3S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="17" related_comp_id="GLC"> <PDBx:atom_id>S2</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="18" related_comp_id="GLC"> <PDBx:atom_id>O4S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="19" related_comp_id="GLC"> <PDBx:atom_id>O5S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="20" related_comp_id="GLC"> <PDBx:atom_id>O6S</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="21" related_comp_id="GLC"> <PDBx:atom_id>H1</PDBx:atom_id> <PDBx:related_atom_id>H1</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="22" related_comp_id="GLC"> <PDBx:atom_id>H2</PDBx:atom_id> <PDBx:related_atom_id>H2</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="23" related_comp_id="GLC"> <PDBx:atom_id>H3</PDBx:atom_id> <PDBx:related_atom_id>H3</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="24" related_comp_id="GLC"> <PDBx:atom_id>H4</PDBx:atom_id> <PDBx:related_atom_id>H4</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="25" related_comp_id="GLC"> <PDBx:atom_id>H5</PDBx:atom_id> <PDBx:related_atom_id>H5</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="26" related_comp_id="GLC"> <PDBx:atom_id>H61</PDBx:atom_id> <PDBx:related_atom_id>H61</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="27" related_comp_id="GLC"> <PDBx:atom_id>H62</PDBx:atom_id> <PDBx:related_atom_id>H62</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="28" related_comp_id="GLC"> <PDBx:atom_id>HN</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="29" related_comp_id="GLC"> <PDBx:atom_id>HO1</PDBx:atom_id> <PDBx:related_atom_id>HO1</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="30" related_comp_id="GLC"> <PDBx:atom_id>HO3</PDBx:atom_id> <PDBx:related_atom_id>HO3</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="31" related_comp_id="GLC"> <PDBx:atom_id>HO4</PDBx:atom_id> <PDBx:related_atom_id>HO4</PDBx:related_atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="32" related_comp_id="GLC"> <PDBx:atom_id>HOS3</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> <PDBx:pdbx_chem_comp_atom_related comp_id="SGN" ordinal="33" related_comp_id="GLC"> <PDBx:atom_id>HOS6</PDBx:atom_id> <PDBx:related_type>Carbohydrate core</PDBx:related_type> </PDBx:pdbx_chem_comp_atom_related> </PDBx:pdbx_chem_comp_atom_relatedCategory> The atom identifier/name for the atom mapping The atom identifier/name for the atom mapping in the related chemical component Describes the type of relationship The chemical component for which this relationship applies. An ordinal index for this category 1 2 The related chemical component for which this chemical component is based. Data items in the PDBX_CHEM_COMP_AUDIT category records the status and tracking information for this component. Example 1 - <PDBx:pdbx_chem_comp_auditCategory> <PDBx:pdbx_chem_comp_audit action_type="Create componenet" comp_id="ATP" date="2007-12-01"> <PDBx:annotator>JY</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_chem_comp_audit> <PDBx:pdbx_chem_comp_audit action_type="Modify leaving atom flag" comp_id="ATP" date="2008-10-03"> <PDBx:annotator>CS</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_chem_comp_audit> <PDBx:pdbx_chem_comp_audit action_type="Modify synonyms" comp_id="ATP" date="2009-07-03"> <PDBx:annotator>MZ</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_chem_comp_audit> </PDBx:pdbx_chem_comp_auditCategory> The initials of the annotator creating of modifying the component. JO SJ KB Additional details decribing this change. Added C14 as a leaving atom. An identifier for the wwPDB site creating or modifying the component. RCSB PDBE PDBJ BMRB PDBC The action associated with this audit record. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The date associated with this audit record. Data items in the PDBX_CHEM_COMP_BOND_EDIT category provide bond level editing instructions to be applied to imported chemical components. Example 1 - <PDBx:pdbx_chem_comp_bond_editCategory> <PDBx:pdbx_chem_comp_bond_edit atom_id_1="OXT" atom_id_2="HXT" comp_id="LYS" edit_op="DELETE"> <PDBx:ordinal>1</PDBx:ordinal> </PDBx:pdbx_chem_comp_bond_edit> </PDBx:pdbx_chem_comp_bond_editCategory> The value for the edited bond property value in the generated component. This data item uniquely identifies and orders each bond edit instruction. The identifier for the first atom in the target bond in imported component. The identifier for the second atom in the target bond in imported component. This data item is a pointer to attribute comp_id in category pdbx_chem_comp_import in the CHEM_COMP category. The operation or assignment applied to the named imported component. Data items in the PDBX_CHEM_COMP_DEPOSITOR_INFO category record additional details provided by depositors about deposited chemical components. Example 1 - <PDBx:pdbx_chem_comp_depositor_infoCategory> <PDBx:pdbx_chem_comp_depositor_info ordinal="1"> <PDBx:alt_comp_id xsi:nil="true" /> <PDBx:comp_id>GNC</PDBx:comp_id> <PDBx:descriptor>CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O</PDBx:descriptor> <PDBx:descriptor_type>SMILES</PDBx:descriptor_type> <PDBx:formula>C8 H15 N O6</PDBx:formula> <PDBx:name>N-acetyl-beta-D-glucosamine</PDBx:name> </PDBx:pdbx_chem_comp_depositor_info> </PDBx:pdbx_chem_comp_depositor_infoCategory> The alternate chemical component identifier matching the deposited chemical component. The chemical component identifier used by the depositor to represent this component. This data item contains the descriptor value for this component. This data item contains the descriptor type. This data item contains additional details about this component. The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S A flag to indicate if the chemical component is defined in the chemical component dictionary. The chemical name of the component. alanine valine adenine cytosine This data item contains the chemical component type. Ordinal index for this category. Data items in the CHEM_COMP_DESCRIPTOR category provide string descriptors of component chemical structure. Example 1 - <PDBx:pdbx_chem_comp_descriptorCategory> <PDBx:pdbx_chem_comp_descriptor comp_id="ATP" program="OPENEYE" program_version="1.5.0" type="SMILES"> <PDBx:descriptor>c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N</PDBx:descriptor> </PDBx:pdbx_chem_comp_descriptor> </PDBx:pdbx_chem_comp_descriptorCategory> This data item contains the descriptor value for this component. Ordinal index for this category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. This data item contains the name of the program or library used to compute the descriptor. OpenEye OECHEM library OPENEYE CACTVS program library CACTVS Daylight program library DAYLIGHT Other program or library OTHER This data item contains the version of the program or library used to compute the descriptor. This data item contains the descriptor type. Additional features associated with the chemical component. Example 1 - <PDBx:pdbx_chem_comp_featureCategory> <PDBx:pdbx_chem_comp_feature comp_id="00X" source="PDB" type="ENZYME INHIBITED" value="ASPARTIC PROTEINASE"></PDBx:pdbx_chem_comp_feature> <PDBx:pdbx_chem_comp_feature comp_id="00X" source="PDB" type="FUNCTION" value="Transistion-state analogue inhibitor"></PDBx:pdbx_chem_comp_feature> <PDBx:pdbx_chem_comp_feature comp_id="00X" source="IUCR" type="STRUCTURE IMAGE URL" value="http://journals.iucr.org/00X.jpg"></PDBx:pdbx_chem_comp_feature> </PDBx:pdbx_chem_comp_featureCategory> The supporting evidence for this feature. Biological assay Data obtained from PNAS August 17, 1999 vol. 96 no. 17 9586-9590 The component identifier for this feature. ABC ATP The information source for the component feature. PDB CHEBI DRUGBANK PUBCHEM The component feature type. CARBOHYDRATE ANOMER CARBOHYDRATE ISOMER CARBOHYDRATE RING The component feature value. Data items in the CHEM_COMP_IDENTIFIER category provide identifiers for chemical components. Example 1 - <PDBx:pdbx_chem_comp_identifierCategory> <PDBx:pdbx_chem_comp_identifier comp_id="ATP" program="ACDLabs" program_version="10.04" type="SYSTEMATIC NAME"> <PDBx:identifier>adenosine 5&apos;-(tetrahydrogen triphosphate)</PDBx:identifier> </PDBx:pdbx_chem_comp_identifier> </PDBx:pdbx_chem_comp_identifierCategory> This data item contains the identifier value for this component. Ordinal index for this category. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. This data item contains the name of the program or library used to compute the identifier. OpenEye OECHEM program OPENEYE Daylight program library DAYLIGHT Advanced Chemistry Development Naming Program ACD Belstein AutoNom Naming Program AUTONOM Compound identifier PUBCHEM_CID Substance identifier PUBCHEM_SID Other program or library OTHER Non-programmatic identifier NONE This data item contains the version of the program or library used to compute the identifier. This data item contains the identifier type. Data items in the PDBX_CHEM_COMP_IMPORT category identify existing chemical components to be imported into the current component definition. Components in this list can be edited by instructions in categories pdbx_chem_comp_atom_edit and pdbx_chem_comp_bond_edit. Example 1 - <PDBx:pdbx_chem_comp_importCategory> <PDBx:pdbx_chem_comp_import comp_id="ATP"></PDBx:pdbx_chem_comp_import> </PDBx:pdbx_chem_comp_importCategory> This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. Data items in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO category records depositor provided information about the chemical context of component instances. Example - <PDBx:pdbx_chem_comp_instance_depositor_infoCategory> <PDBx:pdbx_chem_comp_instance_depositor_info ordinal="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:auth_asym_id>W</PDBx:auth_asym_id> <PDBx:auth_seq_id>102</PDBx:auth_seq_id> <PDBx:author_provided_flag>Y</PDBx:author_provided_flag> <PDBx:comp_id>X78</PDBx:comp_id> <PDBx:in_polymer_flag>N</PDBx:in_polymer_flag> <PDBx:label_alt_id xsi:nil="true" /> </PDBx:pdbx_chem_comp_instance_depositor_info> </PDBx:pdbx_chem_comp_instance_depositor_infoCategory> Optional element of the chemical component instance identifier. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. An element of the chemical component instance identifier. This data item corresponds to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An element of the chemical component instance identifier. This data item corresponds to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A flag to indicate if details about this chemical component instance have been provided by the depositor. An element of the chemical component instance identifier. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. The observed formula for the chemical component in the deposited coordinates. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S A flag to indicate if the chemical component instance is a part of a polymer molecule. An element of the chemical component instance identifier. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The value of pdbx_chem_comp_instance_depositor_info.ordinal must uniquely identify a record in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO list. Data items in the PDBX_CHEM_COMP_MODEL category give details about each of the chemical component model instances. Example 1 - <PDBx:pdbx_chem_comp_modelCategory> <PDBx:pdbx_chem_comp_model id="M_ZZV_00001"> <PDBx:comp_id>ZZV</PDBx:comp_id> </PDBx:pdbx_chem_comp_model> </PDBx:pdbx_chem_comp_modelCategory> An identifier for chemical component definition. ABC The value of attribute id in category pdbx_chem_comp_model must uniquely identify each model instance the PDBX_CHEM_COMP_MODEL list. M_ABC_00001 Data items in the PDBX_CHEM_COMP_MODEL_ATOM category record coordinates for the chemical component model instance. Example 1 - <PDBx:pdbx_chem_comp_model_atomCategory> <PDBx:pdbx_chem_comp_model_atom atom_id="CAA" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>2.180</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>6.561</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>8.402</PDBx:model_Cartn_z> <PDBx:ordinal_id>1</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAB" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>5.709</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>6.659</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>8.211</PDBx:model_Cartn_z> <PDBx:ordinal_id>2</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="OAC" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>1.912</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.185</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>12.303</PDBx:model_Cartn_z> <PDBx:ordinal_id>3</PDBx:ordinal_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="OAD" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.002</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>7.560</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>6.491</PDBx:model_Cartn_z> <PDBx:ordinal_id>4</PDBx:ordinal_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="OAE" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.992</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>9.134</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>8.117</PDBx:model_Cartn_z> <PDBx:ordinal_id>5</PDBx:ordinal_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="OAF" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>2.970</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>10.013</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>13.854</PDBx:model_Cartn_z> <PDBx:ordinal_id>6</PDBx:ordinal_id> <PDBx:type_symbol>O</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="FAG" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>-3.392</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.249</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>6.995</PDBx:model_Cartn_z> <PDBx:ordinal_id>7</PDBx:ordinal_id> <PDBx:type_symbol>F</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAH" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.361</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>5.472</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>12.379</PDBx:model_Cartn_z> <PDBx:ordinal_id>8</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAI" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.277</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>6.182</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>13.595</PDBx:model_Cartn_z> <PDBx:ordinal_id>9</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAJ" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>-2.132</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.408</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>8.958</PDBx:model_Cartn_z> <PDBx:ordinal_id>10</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAK" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>-1.112</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.651</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>6.807</PDBx:model_Cartn_z> <PDBx:ordinal_id>11</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAL" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>-0.902</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.579</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>9.557</PDBx:model_Cartn_z> <PDBx:ordinal_id>12</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAM" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>0.139</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>12.801</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>7.421</PDBx:model_Cartn_z> <PDBx:ordinal_id>13</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> <PDBx:pdbx_chem_comp_model_atom atom_id="CAN" model_id="M_ZZV_00001"> <PDBx:charge>0</PDBx:charge> <PDBx:model_Cartn_x>4.004</PDBx:model_Cartn_x> <PDBx:model_Cartn_y>6.101</PDBx:model_Cartn_y> <PDBx:model_Cartn_z>11.237</PDBx:model_Cartn_z> <PDBx:ordinal_id>14</PDBx:ordinal_id> <PDBx:type_symbol>C</PDBx:type_symbol> </PDBx:pdbx_chem_comp_model_atom> </PDBx:pdbx_chem_comp_model_atomCategory> The net integer charge assigned to this atom. This is the formal charge assignment normally found in chemical diagrams. for an ammonium nitrogen 1 for a chloride ion -1 The x component of the coordinates for this atom in this component model specified as orthogonal angstroms. The y component of the coordinates for this atom in this component model specified as orthogonal angstroms. The z component of the coordinates for this atom in this component model specified as orthogonal angstroms. The value of attribute ordinal_id in category pdbx_chem_comp_model_atom is an ordinal identifer for each atom in the PDBX_CHEM_COMP_MODEL_ATOM list. The code used to identify the atom species representing this atom type. Normally this code is the element symbol. C N O The value of attribute atom_id in category pdbx_chem_comp_model_atom uniquely identifies each atom in the PDBX_CHEM_COMP_MODEL_ATOM list. This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL category. Data items in the PDBX_CHEM_COMP_MODEL_AUDIT category records the status and tracking information for this component model instance. Example 1 - <PDBx:pdbx_chem_comp_model_auditCategory> <PDBx:pdbx_chem_comp_model_audit action_type="Create component model" date="2014-11-30" model_id="M_ZZV_00001"> <PDBx:annotator>JDW</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_chem_comp_model_audit> </PDBx:pdbx_chem_comp_model_auditCategory> The initials of the annotator creating of modifying the component. JO SJ KB Additional details decribing this change. Added C14 as a leaving atom. An identifier for the wwPDB site creating or modifying the component. RCSB PDBE PDBJ BMRB PDBC The action associated with this audit record. The date associated with this audit record. This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL category. Data items in the PDBX_CHEM_COMP_MODEL_BOND category record details about the bonds between atoms in a chemical component model instance. Example 1 - <PDBx:pdbx_chem_comp_model_bondCategory> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="NBA" model_id="M_ZZV_00001"> <PDBx:ordinal_id>1</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAA" model_id="M_ZZV_00001"> <PDBx:ordinal_id>2</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAAA" model_id="M_ZZV_00001"> <PDBx:ordinal_id>3</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAA" atom_id_2="HAAB" model_id="M_ZZV_00001"> <PDBx:ordinal_id>4</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="SBC" model_id="M_ZZV_00001"> <PDBx:ordinal_id>5</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HAB" model_id="M_ZZV_00001"> <PDBx:ordinal_id>6</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HABA" model_id="M_ZZV_00001"> <PDBx:ordinal_id>7</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAB" atom_id_2="HABB" model_id="M_ZZV_00001"> <PDBx:ordinal_id>8</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAC" atom_id_2="CAR" model_id="M_ZZV_00001"> <PDBx:ordinal_id>9</PDBx:ordinal_id> <PDBx:value_order>DOUB</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAD" atom_id_2="SBC" model_id="M_ZZV_00001"> <PDBx:ordinal_id>10</PDBx:ordinal_id> <PDBx:value_order>DOUB</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAE" atom_id_2="SBC" model_id="M_ZZV_00001"> <PDBx:ordinal_id>11</PDBx:ordinal_id> <PDBx:value_order>DOUB</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAF" atom_id_2="CAU" model_id="M_ZZV_00001"> <PDBx:ordinal_id>12</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="OAF" atom_id_2="HOAF" model_id="M_ZZV_00001"> <PDBx:ordinal_id>13</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="FAG" atom_id_2="CAS" model_id="M_ZZV_00001"> <PDBx:ordinal_id>14</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="CAI" model_id="M_ZZV_00001"> <PDBx:ordinal_id>15</PDBx:ordinal_id> <PDBx:value_order>DOUB</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="CAN" model_id="M_ZZV_00001"> <PDBx:ordinal_id>16</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAH" atom_id_2="HAH" model_id="M_ZZV_00001"> <PDBx:ordinal_id>17</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAI" atom_id_2="NAQ" model_id="M_ZZV_00001"> <PDBx:ordinal_id>18</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> <PDBx:pdbx_chem_comp_model_bond atom_id_1="CAI" atom_id_2="HAI" model_id="M_ZZV_00001"> <PDBx:ordinal_id>19</PDBx:ordinal_id> <PDBx:value_order>SING</PDBx:value_order> </PDBx:pdbx_chem_comp_model_bond> </PDBx:pdbx_chem_comp_model_bondCategory> The value of attribute ordinal_id in category pdbx_chem_comp_model_bond is an ordinal identifer for each atom in the PDBX_CHEM_COMP_MODEL_BOND list. The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a bond order. The ID of the first of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category pdbx_chem_comp_model_atom in the PDBX_CHEM_COMP_MODEL_ATOM category. The ID of the second of the two atoms that define the bond. This data item is a pointer to attribute atom_id in category pdbx_chem_comp_model_atom in the PDBX_CHEM_COMP_MODEL_ATOM category. This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL category. Data items in the CHEM_COMP_MODEL_DESCRIPTOR category provide string descriptors for component model structures. Example 1 - <PDBx:pdbx_chem_comp_model_descriptorCategory> <PDBx:pdbx_chem_comp_model_descriptor model_id="M_ZZV_00001" type="SMILES"> <PDBx:descriptor>CN(c1c2cccnc2c(c3c1CN(C3=O)Cc4ccc(cc4)F)O)S(=O)(=O)C</PDBx:descriptor> </PDBx:pdbx_chem_comp_model_descriptor> <PDBx:pdbx_chem_comp_model_descriptor model_id="M_ZZV_00001" type="SMILES_CANNONICAL"> <PDBx:descriptor>CN(c1c2cccnc2c(c3c1CN(C3=O)Cc4ccc(cc4)F)O)S(=O)(=O)C</PDBx:descriptor> </PDBx:pdbx_chem_comp_model_descriptor> </PDBx:pdbx_chem_comp_model_descriptorCategory> This data item contains the descriptor value for this component. This data item is a pointer to attribute id in category pdbx_chem_comp_model in the PDBX_CHEM_COMP_MODEL category. This data item contains the descriptor type. Additional features associated with the chemical component. Example 1 - <PDBx:pdbx_chem_comp_model_featureCategory> <PDBx:pdbx_chem_comp_model_feature feature_name="experiment_temperature" model_id="M_ZZV_00001"> <PDBx:feature_value>218.0</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> <PDBx:pdbx_chem_comp_model_feature feature_name="publication_doi" model_id="M_ZZV_00001"> <PDBx:feature_value>10.1016/j.bmcl.2008.01.018</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> <PDBx:pdbx_chem_comp_model_feature feature_name="r_factor" model_id="M_ZZV_00001"> <PDBx:feature_value>6.92</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> <PDBx:pdbx_chem_comp_model_feature feature_name="all_atoms_have_sites" model_id="M_ZZV_00001"> <PDBx:feature_value>Y</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> <PDBx:pdbx_chem_comp_model_feature feature_name="has_disorder" model_id="M_ZZV_00001"> <PDBx:feature_value>Y</PDBx:feature_value> </PDBx:pdbx_chem_comp_model_feature> </PDBx:pdbx_chem_comp_model_featureCategory> The component feature value. The component model feature type. experiment_temperature publication_doi r_factor all_atoms_have_sites has_disorder The component model identifier for this feature. M_ABC_00001 M_ATP_00001 Additional features associated with the chemical component. Example 1 - <PDBx:pdbx_chem_comp_model_referenceCategory> <PDBx:pdbx_chem_comp_model_reference db_code="PIWVIB" db_name="CSD" model_id="M_ZZV_00001"></PDBx:pdbx_chem_comp_model_reference> </PDBx:pdbx_chem_comp_model_referenceCategory> The component feature value. The component model feature type. CSD The component model identifier for this feature. M_ABC_00001 M_ATP_00001 Data items in the PDBX_CHEM_COMP_NONSTANDARD category describes common nucleotide modifications and nonstandard features. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. This data item describes modification type. PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components. Example 1 - <PDBx:pdbx_chem_comp_relatedCategory> <PDBx:pdbx_chem_comp_related comp_id="SGN" related_comp_id="GLC" relationship_type="Carbohydrate core"> </PDBx:pdbx_chem_comp_related> </PDBx:pdbx_chem_comp_relatedCategory> Describes the type of relationship The chemical component for which this relationship applies. The related chemical component for which this chemical component is based. Describes the type of relationship Data items in the pdbx_chem_comp_subcomponent_entity_list category list the constituent chemical entities and entity features in this chemical component. Example 1 - <PDBx:pdbx_chem_comp_subcomponent_entity_listCategory> <PDBx:pdbx_chem_comp_subcomponent_entity_list id="1"> <PDBx:class>polymer</PDBx:class> <PDBx:parent_comp_id>CE8</PDBx:parent_comp_id> <PDBx:type>saccharide</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_entity_list> </PDBx:pdbx_chem_comp_subcomponent_entity_listCategory> Defines the predominant linking type of the entity. The parent component identifier corresponding to this entity. Defines the type of the entity. Ordinal index for the entities listed in this category. Data items in the pdbx_chem_comp_subcomponent_struct_conn list the chemical interactions among the subcomponents in the chemical component. Example 1 - <PDBx:pdbx_chem_comp_subcomponent_struct_connCategory> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="1"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>1</PDBx:seq_id_1> <PDBx:seq_id_2>2</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="2"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>2</PDBx:seq_id_1> <PDBx:seq_id_2>3</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="3"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>3</PDBx:seq_id_1> <PDBx:seq_id_2>4</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="4"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>4</PDBx:seq_id_1> <PDBx:seq_id_2>5</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="5"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>5</PDBx:seq_id_1> <PDBx:seq_id_2>6</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="6"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>6</PDBx:seq_id_1> <PDBx:seq_id_2>7</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> <PDBx:pdbx_chem_comp_subcomponent_struct_conn id="7"> <PDBx:atom_id_1> O4</PDBx:atom_id_1> <PDBx:atom_id_2> C1</PDBx:atom_id_2> <PDBx:comp_id_1>BGC</PDBx:comp_id_1> <PDBx:comp_id_2>BGC</PDBx:comp_id_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>1</PDBx:entity_id_2> <PDBx:seq_id_1>7</PDBx:seq_id_1> <PDBx:seq_id_2>8</PDBx:seq_id_2> <PDBx:type>covale</PDBx:type> </PDBx:pdbx_chem_comp_subcomponent_struct_conn> </PDBx:pdbx_chem_comp_subcomponent_struct_connCategory> The atom identifier for the first atom in the interaction. The atom identifier for the second atom in the interaction. The component identifier for the first atom in the interaction. The component identifier for the second atom in the interaction. The entity identifier for the first atom in the interaction. The entity identifier for the second atom in the interaction. The positional index for the first atom in the interaction. The positional index for the first atom in the interaction. The chemical or structural type of the interaction. Ordinal index for the interactions listed in this category. PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences. Example 1 - <PDBx:pdbx_chem_comp_synonymsCategory> <PDBx:pdbx_chem_comp_synonyms comp_id="ROC" ordinal="1"> <PDBx:name>Fortovase</PDBx:name> <PDBx:provenance>DRUGBANK</PDBx:provenance> </PDBx:pdbx_chem_comp_synonyms> <PDBx:pdbx_chem_comp_synonyms comp_id="ROC" ordinal="2"> <PDBx:name>SAQUINAVIR</PDBx:name> <PDBx:provenance>DRUGBANK</PDBx:provenance> </PDBx:pdbx_chem_comp_synonyms> <PDBx:pdbx_chem_comp_synonyms comp_id="ROC" ordinal="3"> <PDBx:name>RO 31-8959</PDBx:name> </PDBx:pdbx_chem_comp_synonyms> </PDBx:pdbx_chem_comp_synonymsCategory> The synonym of this particular chemical component. The provenance of this synonym. The type of this synonym. Preferred Trade name The chemical component for which this synonym applies. An ordinal index for this category Data items in the PDBX_CHEM_COMP_UPLOAD_DEPOSITOR_INFO category record details of the uploaded files related to depositor provided chemical assignments. Example 1 - <PDBx:pdbx_chem_comp_upload_depositor_infoCategory> <PDBx:pdbx_chem_comp_upload_depositor_info ordinal="1"> <PDBx:comp_id>GNC</PDBx:comp_id> <PDBx:upload_file_name>GNC.gif</PDBx:upload_file_name> <PDBx:upload_file_type>GIF</PDBx:upload_file_type> </PDBx:pdbx_chem_comp_upload_depositor_info> </PDBx:pdbx_chem_comp_upload_depositor_infoCategory> The chemical component identifier used by the depositor to represent this component. The name of the uploaded file containing information about this component. The type of the uploaded file containing information about this component. Ordinal index for this category. <PDBx:pdbx_columninfoCategory> <PDBx:pdbx_columninfo columnname="id" tablename="summary"> <PDBx:WWW_Report_Criteria>1</PDBx:WWW_Report_Criteria> <PDBx:WWW_Selection_Criteria>1</PDBx:WWW_Selection_Criteria> <PDBx:column_serial_no>1</PDBx:column_serial_no> <PDBx:description>id code</PDBx:description> <PDBx:example>id1, id2</PDBx:example> <PDBx:table_serial_no>1</PDBx:table_serial_no> <PDBx:type>1</PDBx:type> </PDBx:pdbx_columninfo> </PDBx:pdbx_columninfoCategory> SQL column visibility in WWW reports queries. 0=no, 1=yes SQL column visibility in WWW selection querires. 0=no, 1=yes SQL column serial number. 1,2,3,4,... SQL column description. Table of solvent coordinates SQL column example. Table of solvent coordinates SQL table serial number. 1,2,3,4,... SQL column type. 1:integer, 2:float, 3:string-single-left, 4:string-single-right, 5:string-multi-left, 6:string-multi-right, 7:angle, 8:boolean, 9:single character, 10:author or atom name column, 11: Date SQL column name. id SQL table name. structure_summary Local data items describing ligand and monomer chemical features. Internal classification type 1. Internal classification type 2. Date added. Formal charge if nonzero Place-holder for PDB record FORMUL Place-holder for PDB record HETNAM Place-holder for PDB record HET Date of last modification. Parent residue Release status associated with this component. Approximately corresponds to attribute type in category chem_comp Unique (typically 3-letter code) identifier for chemical group. Local data items describing ligand and monomer atom names and connectivity. Starting column of atom name in PDB atom field. Bond type. Charge Element symbol Uniquely identifies the atom within the component. Identifies a connected atom within the component. Unique (typically 3-letter code) identifier for chemical group. Local data items describing ligand and monomer modifications. Type of modification Unique (typically 3-letter code) identifier for chemical group. Local data items describing ligand and monomer type information. Indicates a modified chemical component. Internal chemical type identifier used by NDB. Unique (typically 3-letter code) identifier for chemical group. Data items in the PDBX_CONSTRUCT category specify a sequence of nucleic acids or amino acids. It is a catch-all that may be used to provide details of sequences known to be relevant to the project as well as primers, plasmids, proteins and such like that are either used or produced during the protein production process. Molecules described here are not necessarily complete, so for instance it would be possible to include either a complete plasmid or just its insert. This category may be considered as an abbreviated form of _entity where the molecules described are not required to appear in the final co-ordinates. Note that the details provided here all pertain to a single entry as defined at deposition. It is anticipated that attribute id in category pdbx_construct would also be composed of a sequence that is unique within a given site prefixed by a code that identifies that site and would, therefore, be GLOBALLY unique. Thus this category could also be used locally to store details about the different constructs used during protein production without reference to the entry_id (which only becomes a meaningful concept during deposition). Example 1 - hypothetical example <PDBx:pdbx_constructCategory> <PDBx:pdbx_construct id="1"> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:seq> gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg # - - - - data truncated for brevity - - - -</PDBx:seq> <PDBx:type>DNA</PDBx:type> </PDBx:pdbx_construct> </PDBx:pdbx_constructCategory> The primary function of the construct. This should be considered as a guideline only. The date that the sequence was determined. 2003-12-25 2003-12-25:09:00 Additional details about the construct that cannot be represented in the category _pdbx_construct_feature. In cases where the construct IS found in the co-ordinates then this item provides a pointer to attribute id in category entity in the ENTITY category for the corresponding molecule. The value of attribute entry_id in category pdbx_construct uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. attribute name in category pdbx_construct provides a placeholder for the local name of the construct, for example the plasmid name if this category is used to list plasmids. attribute organisation in category pdbx_construct describes the organisation in which the attribute id in category pdbx_construct is unique. This will normally be the lab in which the constrcut originated. It is envisaged that this item will permit a globally unique identifier to be constructed in cases where this is not possible from the attribute id in category pdbx_construct alone. In cases where the sequence has been determined by a robot this data item provides a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category for the robot responsible sequence expressed as string of one-letter base codes or one letter amino acid codes. Unusual residues may be represented either using the appropriate one letter code wild cards or by the three letter code in parentheses. gatgctgtag gcataggctt ggttatgccg gtactgccgg gcctcttgcg ggatatcgtc gctcaaggcg cactcccgtt ctggataatg ttttttgcgc cgacatcata acggttctgg caaatattct gaaatgagct gttgacaatt aatcatcgat aagcttcttg The type of nucleic acid sequence in the construct. Note that to find all the DNA molecules it is necessary to search for DNA + cDNA and for RNA, RNA + mRNA + tRNA. The value of attribute id in category pdbx_construct must uniquely identify a record in the PDBX_CONSTRUCT list and should be arranged so that it is composed of a site-speicific prefix combined with a value that is unique within a given site.Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_CONSTRUCT_FEATURE category may be used to specify various properties of a nucleic acid sequence used during protein production. Example 1 - vector pUC28 <PDBx:pdbx_construct_featureCategory> <PDBx:pdbx_construct_feature construct_id="1" id="1"> <PDBx:details>pKK84-1 ClaI 5260bp 5247..5247 ptac11 TaqI-TaqI 192bp, -35 trp promoter -&gt; pEA300 5452bp</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type xsi:nil="true" /> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="2"> <PDBx:details>pKK84-1 1..5246 5246bp ClaI = AT^CGAT TaqI = T^CGA cgact...</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type xsi:nil="true" /> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="3"> <PDBx:details>ptac11 190bp ...cat TaqI = T^CGA ClaI = AT^CGAT</PDBx:details> <PDBx:end_seq>5436</PDBx:end_seq> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq>5247</PDBx:start_seq> <PDBx:type xsi:nil="true" /> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="4"> <PDBx:details>pKK84-1 5247..5260 14bp</PDBx:details> <PDBx:end_seq>5450</PDBx:end_seq> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq>5437</PDBx:start_seq> <PDBx:type xsi:nil="true" /> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="5"> <PDBx:details>SIT unique EcoRI-ClaI-HindIII-BamHI-PvuII</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type>misc_binding</PDBx:type> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="6"> <PDBx:details>ORI E. coli pMB1 (ColE1 and pBR322)</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type>rep_origin</PDBx:type> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="7"> <PDBx:details>PRO E. coli trp</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type>promoter</PDBx:type> </PDBx:pdbx_construct_feature> <PDBx:pdbx_construct_feature construct_id="1" id="8"> <PDBx:details>ANT E. coli beta-lactamase gene (bla) ampicillin resistance gene (apr/amp)</PDBx:details> <PDBx:end_seq xsi:nil="true" /> <PDBx:entry_id>111000111</PDBx:entry_id> <PDBx:start_seq xsi:nil="true" /> <PDBx:type>CDS</PDBx:type> </PDBx:pdbx_construct_feature> </PDBx:pdbx_construct_featureCategory> Details that describe the feature The sequence position at which the feature ends The value of attribute entry_id in category pdbx_construct_feature uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. The sequence position at which the feature begins The type of the feature The value of attribute construct_id in category pdbx_construct_feature uniquely identifies the construct with which the feature is associated. This is a pointer to attribute id in category pdbx_construct This item may be a site dependent bar code. The value of attribute id in category pdbx_construct_feature must uniquely identify a record in the PDBX_CONSTRUCT_FEATURE list. Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block. This category atomizes information to a greater degree than the standard AUDIT_CONTACT_AUTHOR category. Example 1 - <PDBx:pdbx_contact_authorCategory> <PDBx:pdbx_contact_author id="1"> <PDBx:address_1>Department of Biophysical Chemistry</PDBx:address_1> <PDBx:address_2>Merck Research Laboratories</PDBx:address_2> <PDBx:address_3>P. O. Box 2000, Ry80M203</PDBx:address_3> <PDBx:city>Rahway</PDBx:city> <PDBx:country>UNITED STATES</PDBx:country> <PDBx:email>paula_fitzgerald@merck.com</PDBx:email> <PDBx:fax>908 594 6645</PDBx:fax> <PDBx:name_first>Paula</PDBx:name_first> <PDBx:name_last>Fitzgerald</PDBx:name_last> <PDBx:name_mi>M.D.</PDBx:name_mi> <PDBx:name_salutation>Dr.</PDBx:name_salutation> <PDBx:organization_type>commercial</PDBx:organization_type> <PDBx:phone>908 594 5510</PDBx:phone> <PDBx:postal_code>07065</PDBx:postal_code> <PDBx:role>principal investigator/group leader</PDBx:role> <PDBx:state_province>New Jersey</PDBx:state_province> </PDBx:pdbx_contact_author> </PDBx:pdbx_contact_authorCategory> The mailing address of the author of the data block to whom correspondence should be addressed, line 1 of 3. 610 Taylor Road The mailing address of the author of the data block to whom correspondence should be addressed, line 2 of 3. Department of Chemistry and Chemical Biology The mailing address of the author of the data block to whom correspondence should be addressed, line 3 of 3. Busch Campus The mailing address of the author of the data block to whom correspondence should be addressed, city. Piscataway The continent of the author of the data block to whom correspondence should be addressed. AFRICA ANTARTICA ASIA AUSTRALIA EUROPE NORTH AMERICA SOUTH AMERICA The country/region of the author of the data block to whom correspondence should be addressed. UNITED STATES UNITED KINGDOM AUSTRALIA The electronic mail address of the author of the data block to whom correspondence should be addressed, in a form recognisable to international networks. name@host.domain.country bm@iucr.ac.uk The facsimile telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number with no spaces. 12(34) 947 7334 732 445 0103 The Open Researcher and Contributor ID (ORCID). 0000-0002-6681-547X The mailing address of the author of the data block to whom correspondence should be addressed transfered from attribute address in category audit_contact_author Busch Campus The first name of the author of the data block to whom correspondence should be addressed. Percival Loyd Susan The last name of the author of the data block to whom correspondence should be addressed. Samuels Rodgers The middle initial(s) of the author of the data block to whom correspondence should be addressed. T. M.F. The salutation of the author of the data block to whom correspondence should be addressed. Dr. Prof. Mr. Ms. Mrs. The organization type to which this author is affiliated. academic commercial government other The telephone number of the author of the data block to whom correspondence should be addressed. The recommended style includes the international dialing prefix, the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefixes in parentheses is no longer recommended. 12 (34) 947 7330 947 732 0103 x8320 The mailing address of the author of the data block to whom correspondence should be addressed, zip code. 08854 The role of this author in the project depositing this data. principal investigator/group leader responsible scientist investigator The mailing address of the author of the data block to whom correspondence should be addressed, state or province. New Jersey A unique integer identifier for this author 1 2 3 Gives information about what kind of coordinates are available. Gives information if the coordinates for the main chain atoms are available. Y Gives information if the coordinates for hydrogen atoms are available. Y Gives information if the coordinates for solvent atoms are available. Y Gives information if the structure factors for this entry are available. Y The entry identifier. The details of the composition of the coordinate model. Example 1 - <PDBx:pdbx_coordinate_modelCategory> <PDBx:pdbx_coordinate_model asym_id="A"> <PDBx:type>CA ATOMS ONLY</PDBx:type> </PDBx:pdbx_coordinate_model> <PDBx:pdbx_coordinate_model asym_id="B"> <PDBx:type>CA ATOMS ONLY</PDBx:type> </PDBx:pdbx_coordinate_model> <PDBx:pdbx_coordinate_model asym_id="X"> <PDBx:type>P ATOMS ONLY</PDBx:type> </PDBx:pdbx_coordinate_model> <PDBx:pdbx_coordinate_model asym_id="Y"> <PDBx:type>P ATOMS ONLY</PDBx:type> </PDBx:pdbx_coordinate_model> </PDBx:pdbx_coordinate_modelCategory> A classification of the composition of the coordinate model. CA ATOMS ONLY P ATOMS ONLY A reference to attribute id in category struct_asym. 1 A Data in the PDBX_CRYSTAL_ALIGNMENT are produced by log files from programs during indexing Angular spread (in degrees) of incident X-ray along the horizontal (x) direction. Default is 0. The estimated deviation of angular spread (in degrees) of incident X-ray along the horizontal (x) direction. Correlated xy component of the beam spread. This tends to be zero within error (in degrees^2). The estimated deviation of correlated xy component of the beam spread (in degrees^2). Angular spread (in degrees) of incident X-ray along the vertical (y) direction. Default is 0. The estimated deviation of angular spread (in degrees) of incident X-ray along the vertical (y) direction. Distance (mm) from crystal to detector. The estimated deviation of distance (mm) from crystal to detector. Crystal mis-orientation angle (in degree) on x axis (spindle). The estimated deviation of orientation angle (in degree) on x axis. Crystal mis-orientation angle (in degree) on y axis (vertical). The estimated deviation of orientation angle (in degree) on y axis. Crystal mis-orientation angle (in degree) on z axis (in beam). The estimated deviation of orientation angle (in degree) on yzaxis. Ending oscillation angle (in degrees) (default end = start + range). The actual oscillation angle (normally <1.0 degree). Starting oscillation angle (in degrees) . Distance (mm) from the edge of data to beam spot (in X direction). The estimated deviation of xbeam (mm). Distance from (mm) the edge of data to beam spot (in Y direction). The estimated deviation of ybeam (mm). The identifer of the crystal. Crystallographic cell specifications used in data processing. Unit cell length A 58.39 Tolerance in unit cell length A 0.04 Unit cell angle alpha. 90.0 Tolerance in unit cell angle alpha. 0.04 Unit cell length B 58.39 Tolerance in unit cell length B 0.04 Unit cell angle beta. 90.0 Tolerance in unit cell angle beta. 0.04 Unit cell length C 58.39 Tolerance in unit cell length C 0.04 Unit cell angle gamma. 90.0 Tolerance in unit cell angle gamma. 0.04 Unit cell mosaicity. 1000.0 Resolution range. 20.0 - edge Space group name. P 21 21 21 Unit cell volume. 245543.0 The value of attribute entry_id in category pdbx_data_processing_cell identifies the data block. Details of the detector used at data collection site. The sample position in the beam in the X direction. 28.026 The sample position in the beam in the Y direction. 31.832 The cassette rotation about the X axis. -0.192 The cassette rotation about the Y axis. -0.238 The cassette rotation about the Z axis. -0.053 The detector crossfire value in the X direction. 0.572 The detector coupled crossfire value for XY. -0.019 The detector crossfire value in the Y direction. 0.504 Identifier for crystal on which data was collected. s04f001.kcd Data collection date. Nov 12, 1999 Name of experimentor. Wladek Minor The name and type of detector. CCD Nonius binned The polarization measured in data collection. -0.03 File system names for the data processing files. s04f001.kcd File system path to processing data files. /u8/wladek/nonius-CDW The value applied to the Y direction. 1.0 The skew value. 0.0 The wavelength of data collection. 0.71074 The value of attribute entry_id in category pdbx_data_processing_detector identifies the data block. Details of reflections used in data processing. Total linear R factor in data processing. 0.021 Total number of reflections used in data processing. 9744 Total number of reflections marked for rejection in data processing. 30 Percent of reflections marked for rejection in data processing. 0.02 Percent of reflections rejected in data processing. 0.01 The value of attribute entry_id in category pdbx_data_processing_reflns identifies the data block. Data items in the PDBX_DATA_PROCESSING_STATUS category record data processing instructions for workflow processing tasks. Example 1 - <PDBx:pdbx_data_processing_statusCategory> <PDBx:pdbx_data_processing_status status="skip" task_name="site"></PDBx:pdbx_data_processing_status> <PDBx:pdbx_data_processing_status status="skip" task_name="link"></PDBx:pdbx_data_processing_status> <PDBx:pdbx_data_processing_status status="skip" task_name="helix"></PDBx:pdbx_data_processing_status> <PDBx:pdbx_data_processing_status status="skip" task_name="solvent position"></PDBx:pdbx_data_processing_status> <PDBx:pdbx_data_processing_status status="skip" task_name="ssbond"></PDBx:pdbx_data_processing_status> </PDBx:pdbx_data_processing_statusCategory> A data processing workflow task status code. skip A data processing workflow task name. site link helix sheet solvent position The PDBX_DATABASE_PDB_MASTER category provides placeholders for the count of various PDB record types. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. The number of PDB records of a particular type. A link to attribute id in category ENTRY The PDBX_DATABASE_PDB_OBS_SPR category provides placeholders for information on obsolete/superseded PDB entries The date of replacement. 1997-03-30 Details related to the replaced or replacing entry. Identifier for the type of obsolete entry to be added to this entry. OBSLTE The new PDB identifier for the replaced entry. 2ABC The PDB identifier for the replaced (OLD) entry/entries. 3ABC Data items in the PDBX_DATABASE_DOI category record the DOI of this entry. Example 1 - pdbx_database_doi <PDBx:pdbx_database_doiCategory> <PDBx:pdbx_database_doi db_name="PDB"> <PDBx:db_DOI>10.2210/pdb6YOX/pdb</PDBx:db_DOI> </PDBx:pdbx_database_doi> </PDBx:pdbx_database_doiCategory> The DOI for the entry in the associated database. 10.2210/pdb6YOX/pdb An abbreviation that identifies the database. The PDBX_DATABASE_MESSAGE category provides information about correspondance related to a structure deposition. This code defines the content of the message. This is the date when a message was sent or received. The text of the message. Defines how the message was sent or received. The name of the receiver. The email address of the receiver. The FAX phone number of the receiver. The postal address of the receiver. The phone number of the receiver. The name of the sender. The email address of the sender. The FAX phone number of the sender. The postal address of the sender. The phone number of the sender. The value of attribute entry_id in category pdbx_database_message identifies the data block. BDL001 This is an unique and sequential identifier for a message. message 1 Data items in the PDBX_DATABASE_PDB_OMIT category record list PDB record names that should be omitted in the PDB format file. <PDBx:pdbx_database_pdb_omitCategory> <PDBx:pdbx_database_pdb_omit entry_id="RCSB00001" record_name="HELIX"></PDBx:pdbx_database_pdb_omit> <PDBx:pdbx_database_pdb_omit entry_id="RCSB00001" record_name="REMARK 500"></PDBx:pdbx_database_pdb_omit> </PDBx:pdbx_database_pdb_omitCategory> The value of attribute entry_id in category pdbx_database_pdb_omit identifies the data block. PDB record or REMARK name to be omitted. Internal records to track the data processing cycle. <PDBx:pdbx_database_procCategory> <PDBx:pdbx_database_proc cycle_id="1" entry_id="BDL001"> <PDBx:date_begin_cycle>1998-02-27</PDBx:date_begin_cycle> <PDBx:date_end_cycle>1998-02-27</PDBx:date_end_cycle> </PDBx:pdbx_database_proc> </PDBx:pdbx_database_procCategory> This is the date of the start of the processing cycle. 1983-02-27 This is the date of the end of the processing cycle. 1983-02-27 Special details about the current processing cycle. This is a number of the processing cycle. 1 for the initial cycle The value of attribute entry_id in category pdbx_database_proc identifies the data block. BDL001 Data items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry. <PDBx:pdbx_database_relatedCategory> <PDBx:pdbx_database_related content_type="native structure" db_id="1ABC" db_name="PDB"></PDBx:pdbx_database_related> </PDBx:pdbx_database_relatedCategory> A description of the related entry. 1ABC contains the same protein complexed with Netropsin. The identifying content type of the related entry. minimized average structure representative structure ensemble derivative structure native structure associated EM volume other EM volume associated NMR restraints associated structure factors associated SAS data protein target sequence and/or protocol data split re-refinement complete structure unspecified other The identifying code in the related database. 1ABC BDL001 The name of the database containing the related entry. PDB - Protein Databank NDB - Nucleic Acid Database BMRB - BioMagResBank EMDB - Electron Microscopy Database BMCD - Biological Macromolecule Crystallization Database TargetTrack - Target Registration and Protocol Database SASBDB - Small Angle Scattering Biological Data Bank Data items in the PDBX_DATABASE_REMARK category record keep additional information about the entry. They are mostly used to create 'non-standard' PDB REMARK annotations (6-99). Example 1 - based on PDB entry 1ABC <PDBx:pdbx_database_remarkCategory> <PDBx:pdbx_database_remark id="1"> <PDBx:text> THE NON-CRYSTALLOGRAPHIC RELATIONSHIP BETWEEN THE THREE DOUBLE HELICES IN THE ASYMMETRIC UNIT IS DESCRIBED IN THE MTRIX1-3 RECORDS.</PDBx:text> </PDBx:pdbx_database_remark> </PDBx:pdbx_database_remarkCategory> The full text of the PDB remark record. A unique identifier for the PDB remark record. These are internal RCSB records to keep track of data processing and status of the entry. <PDBx:pdbx_database_statusCategory> <PDBx:pdbx_database_status entry_id="1ABC"> <PDBx:deposit_site>RCSB</PDBx:deposit_site> <PDBx:process_site>RCSB</PDBx:process_site> <PDBx:status_code>REL</PDBx:status_code> </PDBx:pdbx_database_status> </PDBx:pdbx_database_statusCategory> This code indicates whether the entry belongs to Structural Genomics Project. Y The release date requested by the depositor. This is used when the depositor has provided the release hold date expiration or a one year hold interval. 2016-02-29 This code indicates whether the author's approval for an entry was received explicitly or implicitly. The latter is automatically implied by failure to respond to the validation summary within the prescribed period. implicit = automatic approval by failure to acknowledge explicit = approval via depositor acknowledgement The release status authorized by the depositor. REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor The date on which the depositor accepted the PDB terms and conditions. 2021-09-13 The date the author's approval is received. 1983-02-20 The date on which the author requests entry release. 2013-03-24 The starting date for the deposition session. 2013-02-21 The starting date for data processing. 2013-03-21 The date on which release processing began. 2013-03-24 The date the chemical shift data are received. 2010-02-28 The date the coordinates are received. 1983-02-21 The date the deposition form is received. 1982-02-21 The completion date for data processing. 2013-03-24 At an author's request, the chemical shift data may be held after processing for some period of time. 2010-02-28 At an author's request, a coordinate entry may be held after processing for some period of time. 1983-02-28 At an author's request, the NMR constraint data may be held after processing for some period of time. 1983-02-28 At an author's request, the unified NMR data may be held after processing for some period of time. 2010-02-28 At an author's request, the structure factors may be held after processing for some period of time. 1983-02-28 The date the manuscript is received. 1983-02-28 The date the structure factors are received. 1983-02-28 The date the unified NMR data are received. 2016-02-29 The date of NDB/RCSB release. This corresponds to the date at which the entry is placed into the public archive. 1999-02-28 PDB release date. This is the date that appears in the PDB REVDAT record. 1983-02-28 The date of PDB release. This corresponds to the date at which the chemical shift data is placed into the public archive. 2010-09-28 The date of PDB/RCSB release. This corresponds to the date at which the entry is placed into the public archive. 1999-02-28 The date of PDB release. This corresponds to the date at which the unified NMR data are placed into the public archive. 2010-09-28 The date of PDB/RCSB release. This corresponds to the date at which the entry is placed into the public archive. 1999-02-28 The date on which the entry is sent to PDB. 1999-02-28 The date of a revision. This corresponds to the date at which the entry was updated and a revision entry created. 1983-06-27 The date the structure factors are received. 1983-02-28 The date of complete deposition. This corresponds to the date at which the PDB identifier is assigned. 1983-02-20 The deposited chemical shift data for this deposition will be released according the value of this item. RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 4 WEEKS = Hold for 4 weeks HOLD FOR 6 WEEKS = Hold for 6 weeks HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year The deposited coordinates for this deposition will be released according the value of this item. RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 4 WEEKS = Hold for 4 weeks HOLD FOR 6 WEEKS = Hold for 6 weeks HOLD FOR 8 WEEKS = Hold for 8 weeks HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year The deposited NMR constrait data for this deposition will be released according the value of this item. RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 4 WEEKS = Hold for 4 weeks HOLD FOR 6 WEEKS = Hold for 6 weeks HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year The deposited unified NMR data for this deposition will be released according the value of this item. RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 6 WEEKS = Hold for 6 weeks HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year The sequence information for this deposition will be released according the value of this item. Setting this status code to "RELEASE NOW" indicates that the macromolecular sequence(s) for this entry may be displayed in PDB status reports prior to the release of the entry. Setting this status code to "HOLD FOR RELEASE" conceals the sequence information in PDB status reports until the coordinate data for this entry are released. RELEASE NOW = Release sequence information in status reports immediately HOLD FOR RELEASE = Conceal sequence information in status reports until coordinate data is release The deposited structure factors for this deposition will be released according the value of this item. RELEASE NOW = Release immediately HOLD FOR PUBLICATION = Hold until the primary citation is published HOLD FOR 4 WEEKS = Hold for 4 weeks HOLD FOR 6 WEEKS = Hold for 6 weeks HOLD FOR 8 WEEKS = Hold for 8 weeks HOLD FOR 6 MONTHS = Hold for 6 months HOLD FOR 1 YEAR = Hold for 1 year The site where the file was deposited. NDB RCSB PDBE PDBJ BMRB BNL PDBC At an author's request, an entry is to be held until publication. Y The methods development category in which this entry has been placed. CASP CASD-NMR The last name of the depositor to be used in correspondance. Smith Temporary NDB ID. X96018 This is the date when PDB received the author's approval for an entry which has been processed by NDB. (This is a place holder for entries processed before Jan. 1, 1996.) 1983-02-27 A flag indicating that the entry is compatible with the PDB format. A value of 'N' indicates that the no PDB format data file is corresponding to this entry is available in the PDB archive. Y The initials of the annotator processing this entry. BS SJ KB For author initiated replacement, indicates if new coordinates have been provided Y For author initiated replacement, date new coordinates have been provided 2019-09-28 For author initiated replacement, the current status of the replacement entry PROC = To be processed HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication The site where the file was deposited. NDB RCSB PDBE PDBJ BNL PDBC The initials of the annotator processing this entry. BS SJ KB This code indicates whether the author's approval for an entry has been received. Y This code indicates whether the chemical shift data for an entry have been received. Y This code indicates whether the coordinates for an entry have been received. Y This code indicates whether the deposition form for an entry has been received. Y The date of initial deposition. (The first message for deposition has been received.) 1983-02-21 This code indicates whether the internal approval for an entry have been received. Y This code indicates whether the manuscript for an entry has been received. Y This code indicates whether the NMR contraint data for an entry have been received. Y This code indicates whether the unified NMR data for an entry have been received. Y This code indicates whether the structure factors for an entry have been received. Y The NDB ID that this entry replaced. P001 A description of the revision to this entry. NEW COORDINATES The NDB ID for entry that replaces this entry. P091 This code indicates whether to skip production of a PDB REMARK for this file. 500 This code indicates whether to skip production of PDB REMARK 500 for this file. Y Code for status of file. REL HPUB Code for status of chemical shift data file. PROC = Processing in progress WAIT = Awaiting author approval REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor Code for status of NMR constraints file. PROC = To be processed REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor WAIT = Awaiting author approval Code for status of unified NMR data file. PROC = Processing in progress WAIT = Awaiting author approval REL = Release HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor Code for status of structure factor file. PROC = To be processed REL = Released HOLD = On hold until yyyy-mm-dd HPUB = On hold until publication OBS = Entry has been obsoleted and replaced by another entry WDRN = Entry has been withdrawn by depositor WAIT = Awaiting author approval Give information about status of coordinates of an entry in NDB. Y This code indicates whether to suppress the entry title. Y The value of attribute entry_id in category pdbx_database_status identifies the data block. BDL001 The pdbx_database_status_history category records the time evolution of entry processing status. <PDBx:pdbx_database_status_historyCategory> <PDBx:pdbx_database_status_history entry_id="D_0000000000" ordinal="1"> <PDBx:date_begin>2014-01-01</PDBx:date_begin> <PDBx:date_end>2014-01-01</PDBx:date_end> <PDBx:status_code>PROC</PDBx:status_code> </PDBx:pdbx_database_status_history> </PDBx:pdbx_database_status_historyCategory> This is the date of the start of the current processing status state. 2014-01-29 This is the date of the end of the current processing status state. 2014-01-30 Special details about the current process status state. Current entry processing status. PROC WAIT The value of attribute entry_id in category pdbx_database_status_history identifies the entry data block. D_0000000000 Ordinal index for the status history list. 1 These records are used in the DBREF record of a PDB file and are used as place holders for NDB ID's in PDB files. Example 1 - based on NDB entry BDLB58 <PDBx:pdbx_dbrefCategory> <PDBx:pdbx_dbref begin_res_number="1" chain_id="A" database_name="NDB" end_res_number="12" pdb_id_code="218D"> <PDBx:database_accession>BDLB58</PDBx:database_accession> <PDBx:database_begin_res_number>1</PDBx:database_begin_res_number> <PDBx:database_end_res_number>12</PDBx:database_end_res_number> <PDBx:database_id_code>BDLB58</PDBx:database_id_code> </PDBx:pdbx_dbref> <PDBx:pdbx_dbref begin_res_number="13" chain_id="B" database_name="NDB" end_res_number="24" pdb_id_code="218D"> <PDBx:database_accession>BDLB58</PDBx:database_accession> <PDBx:database_begin_res_number>13</PDBx:database_begin_res_number> <PDBx:database_end_res_number>24</PDBx:database_end_res_number> <PDBx:database_id_code>BDLB58</PDBx:database_id_code> </PDBx:pdbx_dbref> </PDBx:pdbx_dbrefCategory> Insertion code. Database accession. Insertion code. First residue number. Insertion code. Last residue number. Database id code. Insertion code. First residue number. Chain id. Database name. Last residue number. PDB id code. Data items in the category record various overall metrics calculated by DCC and various wrapped programs (such as Xtriage, pointless, REFMAC ...). One of the scale factors used in the bulk solvent correction (from REFMAC). The estimated B factor from the structure factor file by the Wilson plot (from Xtriage). The scale factor for calculating the B factor by the Wilson plot (from Xtriage). The maximum isotropic B factor reported in the model file. The occupancy weighted mean isotropic B factor reported in the model file. The minimum isotropic B factor reported in the model file. The difference between the isotropic B factor and the Bfators from Wilson plot. The DPI on the model determined by REFMAC. The version of the DCC program. The difference of the <I/SigmaI> in the last two points of the plot of <I/SigmaI> vs resolution (expected to be negative). The overall mean value of <I/SigmaI> for the reflections. The <I/SigmaI> at the highest resolution bin calculated by Xtriage. One of the scale factors used in the bulk solvent correction (from REFMAC). The Matthew coefficient. Value of <L^2> calculated by Xtriage using acentric reflections. (untwinned: 0.333; perfect twin: 0.200). Value of <L^2> calculated by Pointless using acentric reflections. (untwinned: 0.333; perfect twin: 0.200). Value of <|L|> calculated by Xtriage using acentric reflections. (untwinned: 0.500; perfect twin: 0.375). The Rfree reported in the model file. The Rwork reported in the model file. The difference between reported Rfree and reported Rwork. Whether TLS was used in refinement. Y for yes, and N for no. Z-scores are computed (by Xtriage) on the basis of a Bernoulli model assuming independence of weak reflections with respect to anisotropy. Multivariate Z score for the L-test calculated by Xtriage using acentric reflections. It is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. The anisotropy ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) calculated by Xtriage. The overall electron density correlation coefficient. The DPI calculated based on the free set, determined by REFMAC. Details of any error or warning messages. The mean figure of merit after refinement. The number of unique reflections for calculating Rfree (testing set) reported in the model file. Boolean whether ice ring exists (Y) or not (N) as determined by Xtriage. The type of B factors (partial or full) for the residue. The highest resolution limit reported in the model file. The highest resolution limit calculated from the structure factor file. The lowest resolution limit calculated from the structure factor file. The number of electron density negative peaks less than 3 sigma. The number of electron density positive peaks larger than 3 sigma. The number of electron density negative peaks less than 6 sigma. The number of electron density positive peaks larger than 6 sigma. Value of <|E^2 - 1|> calculated by Xtriage using acentric reflections.(untwinned: 0.736; perfect twin 0.541). Value of <F>^2/<F^2> calculated by Xtriage using acentric reflections.(untwinned: 0.785; perfect twin 0.885). Value of <I^2>/<I>^2 calculated by Xtriage using acentric reflections.(untwinned: 2.000; perfect twin 1.500). Number of matrix for the NCS groups used in refinement. Number of NCS groups used in refinement. The maximum occupancy reported in the model file. The averaged occupancy reported in the model file. The minimum occupancy reported in the model file. Whether attempt to convert the partial to full B factors before validation. Whether the conversion of partial B to full B factor is successful (Y) or not (N). The keywords of the structure (taken from attribute pdbx_keywords) in category struct_keywords. The probability to tell the existence of translational pseudo symmetry. p_values smaller than 0.05 (1e-3) might indicate weak (strong) translational pseudo symmetry (by Xtriage). The overall real space R factor. Whether the status is of reflection is archived (Y) or not (N). Whether the status of the reflection is used (Y) or not (N). Boolean (Y/N) whether the twin is reported. The solvent content. Hermann-Mauguin space-group symbol reported in the model file. Hermann-Mauguin space-group symbol calculated by the POINTLESS program using the structure factor file. Number of TLS groups used in refinement. Boolean whether translational pseudo symmetry exist (Y) or not (N) as determined by Xtriage. The Rfactor calculated by Xtriage using the twin operator related data. (Smaller values indicate twins). Boolean (Y/N) whether twin is detected by Xtriage. Twin fractions determined by REFMAC. The twin fraction determined by Xtriage. Twin operators determined by REFMAC. A list of the twin operators determined by Xtriage. Type of twin (merohedral,Pseudo-merohedral or non-merohedral) determined by Xtriage. The unit cell parameters (a b c alpha beta gamma) separated by a space. The wavelength reported from the model file. The number of unique reflections for refinement (working set) reported in the model file. The PDB id code. Data items in the category record calculated metrics from various programs (such as phenix, refmac, cns, sfcheck). The overall real space density correlation coefficient. The correlations between the observed and calculated structure factors. Any additional details of the calculations. The calculated Rfactor using all the data. The calculated Rfree using the test set data. The calculated Rfactor using the working set data. The highest resolution limit in calculating the metrics in this category. The lowest resolution limit in calculating the metrics in this category. The number of reflections for the test set only. The number of unique reflections (work+test sets). The percentage of unique reflections (work+test sets). The program used to calculate the metrics in this category. The overall real space R factor. The ordered number in the output list. Data items in the category record the overall deviations about geometry (such as bond length, angle, dihedral, chirality, planarity). These data are calculated with the phenix module model_vs_data. Number of allowed residues in Ramachandran plot. Percentage of allowed residues in Ramachandran plot. Number of favored residues in Ramachandran plot. Percentage of favored residues in Ramachandran plot. Number of outliers in Ramachandran plot. Percentage of outliers in Ramachandran plot. All atom score is determined by steric overlaps >0.4A per 1000 atoms. The maximum root mean square deviation for bond angles (ligand only). The overall root mean square deviation for bond angles (ligand only). The maximum root mean square deviation for bond angles (all atoms). The overall root mean square deviation for bond angles (all atoms). The maximum root mean square deviation for bond lengths (ligand only). The overall root mean square deviation for bond lengths (ligand only). The maximum root mean square deviation for bond lengths (all atoms). The overall root mean square deviation for bond lengths (all atoms). Number of Cbeta deviations >0.25A. The maximum root mean square deviation for chirality (all atoms). The overall root mean square deviation for chirality (all atoms). The maximum root mean square deviation for dihedrals (all atoms). The overall root mean square deviation for dihedrals (all atoms). The overall on-bonded distance (all atoms). The overall score for the geometry (the smaller the better). The maximum root mean square deviation for planarity (all atoms). The overall root mean square deviation for planarity (all atoms). Number of rotamer outliers. Percentage of rotamer outliers. The PDB id code. Data items in the category record residual map properties such as Real Space electron density Correlation Coefficient (RSCC), real space R factors (RSR) and the Zscores for each residue, the main/side chains. The occupancy weighted average isotropic B factors for the residue. It is defined as (SUM B*Q)/(SUM Q), where B is the isotropic B factor for each atom and Q is the occupancy. The occupancy weighted average isotropic B factors for the main chain atoms. The occupancy weighted average isotropic B factors for the phosphate atoms. The occupancy weighted average isotropic B factors for the side chain atoms. It is the Ligand Local Density Function defined as the (<RsR>_local - RsR_Ligand)/sigma_RsR, where <RsR>_local is the mean RSR of polymer residues in 5 Angstrom (including the crystallographic symmetry) surrounding the ligand, and sigma_RsR is sigma value calculated from the surrounding residues. The Real Space electron density Correlation Coefficient for the residue. It is defined as RSCC=(<xy>-<x><y>)/[sqrt(<x**2>-<x>**2)*sqrt(<y**2>-<y>**2)] where x is the observed density from the (2mFo-DFc) map and y is the calculated density from the Fc map The Real Space electron density Correlation Coefficient for the main chain atoms. The Real Space electron density Correlation Coefficient for the phosphate atoms. The Real Space electron density Correlation Coefficient for the side chain atoms. The Real space Rfactor (RSR) for the residue. It is defined as RSR=sum(|x-y|/x+y|) which is the summation over all grid points around the residue, where x is the observed density from the (2mFo-DFc) map and y is the calculated density from the Fc map. Zscore of the Real Space Rfactor (RSRZ) for the residue. It is defined as (RSR-<RSR>)/sigma_RSR, where <RSR> and sigma_RSR are for the whole map, RSR is for the residue. Zscore of the Real Space Rfactor (RSRZ) for the main chain atoms. Zscore of the Real Space Rfactor (RSRZ) for the phosphate atoms. Zscore of the Real Space Rfactor (RSRZ) for the side chain atoms. The Real space Rfactor (RSR) for the main chain atoms. The Real space Rfactor (RSR) for the phosphate atoms. The Real space Rfactor (RSR) for the side chain atoms. The real space difference density Z score (defined as Delta_rho/sigma(Delta_rho)) from Tickle (2012). It is related to the model accuracy. RSZD>3, significant extra positive density around the residue; RSZD<-3, significant extra negative density around the residue. The same as attribute RSZD in category pdbx_dcc_map, use for the main chain atoms. The same as attribute RSZD in category pdbx_dcc_map, use for the phosphate atoms of nucleic acids. The same as attribute RSZD in category pdbx_dcc_map, use for the side chain atoms. The real space observed density Z score (defined as <rho_obs>/sigma(Delta_rho)) from Tickle (2012). It is related to the model precision (B factors). Small or large value means weak or strong density for the residue. The Zscore of RSZO (or the Zscore of <rho_obs>/sigma(Delta_rho)). The same as attribute RSZO in category pdbx_dcc_map, use for the main chain atoms. The same as attribute RSZO in category pdbx_dcc_map, use for the phosphate atoms of nucleic acids. The same as attribute RSZO in category pdbx_dcc_map, use for the side chain atoms. The author provided chain id. The author provided compound ID (residue name). The author provided residue number. Defined in sfcheck. It is the product of the (2Fobs-Fcal) electron density values for the backbone atoms N, CA and C, and in the case of RNA/DNA, for P, O5', C5', C3', O3'. Low values of this index indicate breaks in the backbone electron density which may be due to flexibility of the chain or incorrect tracing. Defined in sfcheck. It is the mean density of the main chain atoms divided by the mean density of the map. Defined in sfcheck. It is the mean density of the side chain atoms divided by the mean density of the map. Author provided alternate location identifier. The PDB insertion code. The component model identifier for this analysis. The averaged occupancy for the residue. The averaged occupancy forthe main chain atoms. The averaged occupancy forthe phosphate atoms. The averaged occupancy forthe side chain atoms. The PDB id code (four characters). The value indicates any problems with this group of atoms. If given as 'd', it means there is problem of local model accuracy. If given as 'w', it means weak density (there is problem of local model precision). If given as 'dw', both then problems exist. Defined in sfcheck (displacement/sigma_of_displacement). Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. The same as attribute density_shift in category pdbx_dcc_map, but it is for main chain. The same as attribute density_shift in category pdbx_dcc_map, but it is for side chain. Zscore of weighted Real Space Rfactor (RSR/RSCC) for the main chain atoms. Zscore of weighted Real Space Rfactor (RSR/RSCC) for the phosphate atoms. Zscore of weighted Real Space Rfactor (RSR/RSCC) for the side chain atoms. The weighted Real Space Rfactor (RSR/RSCC) for the main chain atoms. The weighted Real Space Rfactor (RSR/RSCC) for the phosphate atoms. The weighted Real Space Rfactor (RSR/RSCC) for the side chain atoms. The weighted Real Space Rfactor (defined as RSR/RSCC) for the residue. Zscore of weighted Real Space Rfactor for the residue. It is defined as (wRSR-<wRSR>)/sigma_wRSR, where <wRSR> and sigma_wRSR are for the whole map, wRSR is for the residue. The ordered number of residue in the output list. Data items in the category record details from the output of mapman used by the DCC program. The details of the use of mapman by the DCC program. The PDB id code. Data items in this category record residual map properties such as correlation, real space Rfactors and the Zscore calculated from refmac and mapman. The occupancy weighted average isotropic B factors for the residue. The author provided chain id. The author provided compound ID (residue name). The author provided residue number. The real space electron density correlation coefficient (RSCC) for the residue. Residue with density problem will be flagged as P. The author provided alternate location identifier. PDB insertion code. The component model identifier for this analysis. The average occupancy for the residue. The PDB id code. The Real Space Rfactor (RSR) for the residue. The Zscore of the Real Space Rfactor (RSRZ) for the residue. The weighted Real Space Rfactor (RSR/RSCC) for the residue. The ordered number in the output list. Data items in the category record overall map properties such as correlation, real space Rfactors and the Zscore calculated from refmac and mapman. The overall real space electron density correlation coefficient (RSCC) for the structure. The overall standard deviation of the real space electron density correlation coefficient (RSCC) for the structure. The overall Real Space Rfactor (RSR) for the structure. The overall standard deviation of the Real Space Rfactor (RSR) for the structure. The PDB id code. Data items in the pdbx_deposit_group category provide identifiers and related information for groups of entries deposited in a collection. Example 1 - Deposition collection <PDBx:pdbx_deposit_groupCategory> <PDBx:pdbx_deposit_group group_id="B_0000000001"></PDBx:pdbx_deposit_group> </PDBx:pdbx_deposit_groupCategory> A description of the contents of entries in the collection. A title to describe the group of entries deposited in the collection. Text to describe a grouping of entries in multiple collections A unique identifier for a group of entries deposited as a collection. Data items in the pdbx_deposit_group_index category provides details about the individual data files in the collection of deposited entries. Example 1 - Deposition collection <PDBx:pdbx_deposit_group_indexCategory> <PDBx:pdbx_deposit_group_index group_id="B_1000000001" ordinal_id="1"> <PDBx:auth_file_content_type>model</PDBx:auth_file_content_type> <PDBx:auth_file_format_type>cif</PDBx:auth_file_format_type> <PDBx:auth_file_label>model1</PDBx:auth_file_label> <PDBx:auth_file_name>model-file-1.cif</PDBx:auth_file_name> <PDBx:auth_file_size>4000002</PDBx:auth_file_size> <PDBx:dep_set_id>D_2000000001</PDBx:dep_set_id> <PDBx:group_file_name>myset.tar.gz</PDBx:group_file_name> <PDBx:group_file_timestamp>2016-01-02:10:02</PDBx:group_file_timestamp> <PDBx:pdb_id_code>1ABC</PDBx:pdb_id_code> </PDBx:pdbx_deposit_group_index> <PDBx:pdbx_deposit_group_index group_id="B_1000000001" ordinal_id="2"> <PDBx:auth_file_content_type>structure factors</PDBx:auth_file_content_type> <PDBx:auth_file_format_type>cif</PDBx:auth_file_format_type> <PDBx:auth_file_label>sf1</PDBx:auth_file_label> <PDBx:auth_file_name>sf-file-1.cif</PDBx:auth_file_name> <PDBx:auth_file_size>53000022</PDBx:auth_file_size> <PDBx:dep_set_id>D_2000000001</PDBx:dep_set_id> <PDBx:group_file_name>myset.tar.gz</PDBx:group_file_name> <PDBx:group_file_timestamp>2016-01-02:10:02</PDBx:group_file_timestamp> <PDBx:pdb_id_code>1ABC</PDBx:pdb_id_code> </PDBx:pdbx_deposit_group_index> </PDBx:pdbx_deposit_group_indexCategory> The data content type for this data file within the collection. model The data format for this data file within the collection. mmcif A contributor label for this data file within the collection. file1 The file name for this data file within the collection. file-1.cif The file size (bytes) for this data file within the collection. 15000232 An internal identifier for a deposited data set. A file name of the group of collected structures. big-set.tar.gz A file timestamp of the group of collected structures. A PDB accession code. A unique identifier for a group of entries deposited as a collection. A unique identifier for the index entry within the deposition group. Data items in the PDBX_DEPOSITION_MESSAGE_FILE_REFERENCE category record details of files references associated with messages defined in the PDBX_DEPOSITION_MESSAGE_INFO data category. Example 1 - <PDBx:pdbx_deposition_message_file_referenceCategory> <PDBx:pdbx_deposition_message_file_reference ordinal="1"> <PDBx:content_format>pdbx</PDBx:content_format> <PDBx:content_type>model-annotate</PDBx:content_type> <PDBx:deposition_data_set_id>D_000000</PDBx:deposition_data_set_id> <PDBx:message_id>8bf7a60b-066d-4fff-8ee9-c5b820e19b3c</PDBx:message_id> <PDBx:partition_number>1</PDBx:partition_number> <PDBx:storage_type>archive</PDBx:storage_type> <PDBx:version_id>1</PDBx:version_id> </PDBx:pdbx_deposition_message_file_reference> <PDBx:pdbx_deposition_message_file_reference ordinal="2"> <PDBx:content_format>pdbx</PDBx:content_format> <PDBx:content_type>model-annotate</PDBx:content_type> <PDBx:deposition_data_set_id>D_000000</PDBx:deposition_data_set_id> <PDBx:message_id>8bf7a60b-066d-4fff-8ee9-c5b820e19b3c</PDBx:message_id> <PDBx:partition_number>1</PDBx:partition_number> <PDBx:storage_type>archive</PDBx:storage_type> <PDBx:version_id>1</PDBx:version_id> </PDBx:pdbx_deposition_message_file_reference> </PDBx:pdbx_deposition_message_file_referenceCategory> The content format of the referenced data file. The content type of the referenced data file. The internal identifier assigned to each deposition. The internal identifier assigned to each message. The partition number of the referenced data file. The storate type of the referenced data file. The version identifier of the referenced data file. Ordinal index for the each file reference. Data items in the PDBX_DEPOSITION_MESSAGE_INFO category record internal messages within the depositon and annotation system. Example 1 - <PDBx:pdbx_deposition_message_infoCategory> <PDBx:pdbx_deposition_message_info ordinal="1"> <PDBx:content_type>report</PDBx:content_type> <PDBx:content_value>validation</PDBx:content_value> <PDBx:deposition_data_set_id>D_000000</PDBx:deposition_data_set_id> <PDBx:message_id>83ae9530-194c-4360-93d2-90598491012a</PDBx:message_id> <PDBx:message_subject>Response to validation report</PDBx:message_subject> <PDBx:message_text> All of the C-alpha and C-beta atom coordinates have gone missing. We looked all over the lab and could not find them. There were a few reflections that we misplaced earlier. We are hoping that we will find these data before the manuscript is reviewed.</PDBx:message_text> <PDBx:message_type>text</PDBx:message_type> <PDBx:parent_message_id>83ae9530-194c-4360-93d2-90598491012a</PDBx:parent_message_id> <PDBx:send_status>draft</PDBx:send_status> <PDBx:sender>depositor</PDBx:sender> <PDBx:timestamp>2013-08-15 12:49:26</PDBx:timestamp> </PDBx:pdbx_deposition_message_info> </PDBx:pdbx_deposition_message_infoCategory> A the message content type or class. A the specific value of the content type or class The internal identifier assigned to each deposition. The internal identifier assigned to each message. The subject text of the message. The body of the message. The message type. text The identifier of the parent message or the message to which the current message responds. The message status. draft A the message creator. A the date and time of message creation. Ordinal index for the each message. Data items in the PDBX_DEPUI_ENTITY_FEATURES category record status details related to the features of individual entities. Example 1 - <PDBx:pdbx_depui_entity_featuresCategory> <PDBx:pdbx_depui_entity_features dep_dataset_id="D_000000" entity_id="1" type="Antibiotic/inhibitor"></PDBx:pdbx_depui_entity_features> </PDBx:pdbx_depui_entity_featuresCategory> The internal identifier assigned to each deposition. A reference to the attribute id in category entity in the ENTITY category A flag to indicate the molecule class for the entity. Data items in the PDBX_DEPUI_ENTITY_STATUS_FLAGS category record status details related to individual entities. Example 1 - <PDBx:pdbx_depui_entity_status_flagsCategory> <PDBx:pdbx_depui_entity_status_flags dep_dataset_id="D_000000" entity_id="1"> <PDBx:has_mutation>Y</PDBx:has_mutation> </PDBx:pdbx_depui_entity_status_flags> </PDBx:pdbx_depui_entity_status_flagsCategory> A flag to indicate that the entity has a mutation. A flag to indicate that sample and coordinate sequence alignments is valid for this entity The internal identifier assigned to each deposition. A reference to the attribute id in category entity in the ENTITY_POLY category Data items in the PDBX_DEPUI_ENTRY_DETAILS category record information required to identify the depositor and route deposition to an appropriate processing site. Example 1 - <PDBx:pdbx_depui_entry_detailsCategory> <PDBx:pdbx_depui_entry_details dep_dataset_id="D_0000000000"> <PDBx:country>United States</PDBx:country> <PDBx:experimental_methods>X-Ray Diffraction</PDBx:experimental_methods> <PDBx:requested_accession_types>PDB</PDBx:requested_accession_types> <PDBx:validated_contact_email>user@host</PDBx:validated_contact_email> </PDBx:pdbx_depui_entry_details> </PDBx:pdbx_depui_entry_detailsCategory> The country/region location of the institution submitting the deposition. United States United Kingdom Japan Comma separated list of supported experimental methods. X-Ray Diffraction Electron Microscopy Solution NMR Neutron Diffraction Electron Crystallography Solid-state NMR Solution Scattering Fiber Diffraction A database code closely related to the current deposition. 1ABC The name of the database associated with the related database code. EMDB PDB BMRB The PDB ID code of the entry that is superseded by this entry. 1ABC Comma separated list of requested accession code types. PDB EMDB BMRB A flag to indicate the that the deposition is a contribution from a structural genomics project. Y N The validated contact e-mail address for the correponding depositor. user@domain The wwPDB internal site configuration identifier. WWPDB_DEPLOY_C5 WWPDB_DEPLOY_STAGING_RU WWPDB_DEPLOY_ALPHA_RU WWPDB_DEPLOY_TEST_RU WWPDB_DEPLOY_INTERNAL_RU WWPDB_DEPLOY_PRODUCTION_PDBJ WWPDB_DEPLOY_VALSRV_RU WWPDB_DEPLOY_PRODUCTION_RU WWPDB_DEPLOY_PRODUCTION_UCSD WWPDB_DEPLOY_DEVEL_RU WWPDB_DEPLOY_MACOSX PDBE BMRB The internal identifier assigned to each deposition. Data items in the PDBX_DEPUI_STATUS_FLAGS category record status details used to maintain state within the wwPDB deposition system. Example 1 - <PDBx:pdbx_depui_status_flagsCategory> <PDBx:pdbx_depui_status_flags dep_dataset_id="D_000000"> <PDBx:corresponding_author_status>N</PDBx:corresponding_author_status> <PDBx:has_ncs_data>Y</PDBx:has_ncs_data> <PDBx:is_grant_funded>Y</PDBx:is_grant_funded> <PDBx:prediction_target>N</PDBx:prediction_target> <PDBx:primary_citation_status>N</PDBx:primary_citation_status> <PDBx:reference_citation_status>N</PDBx:reference_citation_status> </PDBx:pdbx_depui_status_flags> </PDBx:pdbx_depui_status_flagsCategory> A flag to indicate status about corresponding author data. A flag to indicate that depositor has accepted the presented assemblies. A flag to indicate the acceptance of wwPDB deposition and annotation terms and conditions. A flag to indicate that this entry has cyclic symmetry A flag to indicate that this entry has helical symmetry A flag to indicate that the deposition includes NCS data. A flag to indicate that this entry has point symmetry A flag to indicate whether the author has related SAXS/SANS data. A flag to indicate the viewing the latest validation report. A flag to indicate that the deposition was grant funded. A flag to indicate that ligand processing is complete A flag to indicate whether related SAXS/SANS data is already deposited elsewhere For the last model merge operation, the name of the model file containing output from the merge operation. For the last model merge operation, the name of the model file containing prior data for the current deposition session. For the last model merge operation, the name of the model file containing user provided replacement coordinate and model data. A flag to indicate that merging of new coordinates has failed. Records reason for author initiated coordinate replacement Records additional details for author initiated coordinate replacement A flag to indicate that this entry is a candidate prediction target. A flag to indicate status about primary citation data. A flag to indicate status about reference citation data. A flag to indicate that all sample coordinate sequence alignments are valid. A flag to indicate whether related SAXS/SANS data were used in refinement The last validation report operation, the name of the model file last validated. The internal identifier assigned to each deposition. Data items in the PDBX_DEPUI_UPLOAD category record the details of uploaded data files. Example 1 - <PDBx:pdbx_depui_uploadCategory> <PDBx:pdbx_depui_upload ordinal="1"> <PDBx:file_content_type>PDBx/mmCIF model file</PDBx:file_content_type> <PDBx:file_name>myfile.cif</PDBx:file_name> <PDBx:file_size>34567</PDBx:file_size> <PDBx:file_type>xs-cif</PDBx:file_type> <PDBx:valid_flag>Y</PDBx:valid_flag> </PDBx:pdbx_depui_upload> </PDBx:pdbx_depui_uploadCategory> Text of any diagnostic messages asssociated with the upload processing of the input data. The content type of the uploaded file. PDBx/mmCIF model file PDB model file PDBx/mmCIF structure factor file other The name of the uploaded file. The size of the uploaded file in bytes. The internal file type of the uploaded file. xs-cif other Some text data item related sequene alignment. A flag to indicate if the uploaded data is satisfies a preliminary validation criteria. Ordinal identifier for each update record. Data items in the PDBX_DEPUI_VALIDATION_STATUS_FLAGS category record status details that assess the status of selected validation diagnostics. Example 1 - <PDBx:pdbx_depui_validation_status_flagsCategory> <PDBx:pdbx_depui_validation_status_flags dep_dataset_id="D_000000"> <PDBx:adp_outliers_low>0</PDBx:adp_outliers_low> <PDBx:occupancy_outliers_high>0</PDBx:occupancy_outliers_high> <PDBx:occupancy_outliers_low>0</PDBx:occupancy_outliers_low> <PDBx:solvent_outliers>0</PDBx:solvent_outliers> </PDBx:pdbx_depui_validation_status_flags> </PDBx:pdbx_depui_validation_status_flagsCategory> Count of atoms with ADP (B-values) values less than 0 A flag to indicate if any isotropic B factors are zero. Count of atoms with occupancy values greater than 1 Count of atoms with occupancy values less than 0 A flag to indicate if the uploaded data is contains residual B-values Count of solvent atoms with anonalous positions. A flag to indicate if the uploaded model has TLS records but no anisotropic ones. The internal identifier assigned to each deposition. Data items in the DIFFRN_REFLNS_SHELL category record details about the reflection data set within shells of resolution. Example 1 - diffraction properties with shells <PDBx:pdbx_diffrn_reflns_shellCategory> <PDBx:pdbx_diffrn_reflns_shell d_res_high="5.18" d_res_low="50.00" diffrn_id="1"> <PDBx:Rmerge_I_obs>0.029</PDBx:Rmerge_I_obs> <PDBx:chi_squared>1.154</PDBx:chi_squared> <PDBx:number_obs>11791</PDBx:number_obs> <PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs> </PDBx:pdbx_diffrn_reflns_shell> <PDBx:pdbx_diffrn_reflns_shell d_res_high="4.11" d_res_low="5.18" diffrn_id="1"> <PDBx:Rmerge_I_obs>0.033</PDBx:Rmerge_I_obs> <PDBx:chi_squared>1.098</PDBx:chi_squared> <PDBx:number_obs>11717</PDBx:number_obs> <PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs> </PDBx:pdbx_diffrn_reflns_shell> <PDBx:pdbx_diffrn_reflns_shell d_res_high="3.59" d_res_low="4.11" diffrn_id="1"> <PDBx:Rmerge_I_obs>0.043</PDBx:Rmerge_I_obs> <PDBx:chi_squared>1.044</PDBx:chi_squared> <PDBx:number_obs>11792</PDBx:number_obs> <PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs> </PDBx:pdbx_diffrn_reflns_shell> <PDBx:pdbx_diffrn_reflns_shell d_res_high="3.26" d_res_low="3.59" diffrn_id="1"> <PDBx:Rmerge_I_obs>0.059</PDBx:Rmerge_I_obs> <PDBx:chi_squared>1.104</PDBx:chi_squared> <PDBx:number_obs>11718</PDBx:number_obs> <PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs> </PDBx:pdbx_diffrn_reflns_shell> <PDBx:pdbx_diffrn_reflns_shell d_res_high="3.03" d_res_low="3.26" diffrn_id="1"> <PDBx:Rmerge_I_obs>0.087</PDBx:Rmerge_I_obs> <PDBx:chi_squared>1.160</PDBx:chi_squared> <PDBx:number_obs>11753</PDBx:number_obs> <PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs> </PDBx:pdbx_diffrn_reflns_shell> <PDBx:pdbx_diffrn_reflns_shell d_res_high="2.85" d_res_low="3.03" diffrn_id="1"> <PDBx:Rmerge_I_obs>0.130</PDBx:Rmerge_I_obs> <PDBx:chi_squared>1.169</PDBx:chi_squared> <PDBx:number_obs>11811</PDBx:number_obs> <PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs> </PDBx:pdbx_diffrn_reflns_shell> <PDBx:pdbx_diffrn_reflns_shell d_res_high="2.71" d_res_low="2.85" diffrn_id="1"> <PDBx:Rmerge_I_obs>0.174</PDBx:Rmerge_I_obs> <PDBx:chi_squared>1.170</PDBx:chi_squared> <PDBx:number_obs>11752</PDBx:number_obs> <PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs> </PDBx:pdbx_diffrn_reflns_shell> <PDBx:pdbx_diffrn_reflns_shell d_res_high="2.59" d_res_low="2.71" diffrn_id="1"> <PDBx:Rmerge_I_obs>0.227</PDBx:Rmerge_I_obs> <PDBx:chi_squared>1.165</PDBx:chi_squared> <PDBx:number_obs>11767</PDBx:number_obs> <PDBx:percent_possible_obs>100.000</PDBx:percent_possible_obs> </PDBx:pdbx_diffrn_reflns_shell> </PDBx:pdbx_diffrn_reflns_shellCategory> The R factor for the reflections that satisfy the merging criteria for the resolution shell. The R factor for averaging the symmetry related reflections for the resolution shell. The overall Chi-squared statistic for the resolution shell. The number of observed reflections in the resolution shell. The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by attribute d_resolution_high in category diffrn_reflns_shell and attribute d_resolution_low in category diffrn_reflns_shell and the observation limit established by attribute observed_criterion. in category diffrn_reflns The overall redundancy for the resolution shell. The number of rejected reflections in the resolution shell The highest resolution for the interplanar spacings in the resolution shell. The lowest resolution for the interplanar spacings in the resolution shell. This data item is a pointer to attribute id in category diffrn in the DIFFRN category. This item distingush the different data sets Data items in the PDBX_DISTANT_SOLVENT_ATOMS category list the solvent atoms remote from any macromolecule. Example 1 <PDBx:pdbx_distant_solvent_atomsCategory> <PDBx:pdbx_distant_solvent_atoms id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>W</PDBx:auth_asym_id> <PDBx:auth_atom_id>O</PDBx:auth_atom_id> <PDBx:auth_comp_id>HOH</PDBx:auth_comp_id> <PDBx:auth_seq_id>412</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:neighbor_ligand_distance xsi:nil="true" /> <PDBx:neighbor_macromolecule_distance>7.3</PDBx:neighbor_macromolecule_distance> </PDBx:pdbx_distant_solvent_atoms> <PDBx:pdbx_distant_solvent_atoms id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>W</PDBx:auth_asym_id> <PDBx:auth_atom_id>O</PDBx:auth_atom_id> <PDBx:auth_comp_id>HOH</PDBx:auth_comp_id> <PDBx:auth_seq_id>413</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:neighbor_ligand_distance xsi:nil="true" /> <PDBx:neighbor_macromolecule_distance>8.4</PDBx:neighbor_macromolecule_distance> </PDBx:pdbx_distant_solvent_atoms> <PDBx:pdbx_distant_solvent_atoms id="3"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>W</PDBx:auth_asym_id> <PDBx:auth_atom_id>O</PDBx:auth_atom_id> <PDBx:auth_comp_id>HOH</PDBx:auth_comp_id> <PDBx:auth_seq_id>414</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:neighbor_ligand_distance xsi:nil="true" /> <PDBx:neighbor_macromolecule_distance>7.2</PDBx:neighbor_macromolecule_distance> </PDBx:pdbx_distant_solvent_atoms> <PDBx:pdbx_distant_solvent_atoms id="4"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>W</PDBx:auth_asym_id> <PDBx:auth_atom_id>O</PDBx:auth_atom_id> <PDBx:auth_comp_id>HOH</PDBx:auth_comp_id> <PDBx:auth_seq_id>415</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:neighbor_ligand_distance xsi:nil="true" /> <PDBx:neighbor_macromolecule_distance>8.3</PDBx:neighbor_macromolecule_distance> </PDBx:pdbx_distant_solvent_atoms> </PDBx:pdbx_distant_solvent_atomsCategory> Part of the identifier for the distant solvent atom. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_alt.id in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the distant solvent atom. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Distance to closest neighboring ligand or solvent atom. Distance to closest neighboring macromolecule atom. The value of attribute id in category pdbx_distant_solvent_atoms must uniquely identify each item in the PDBX_DISTANT_SOLVENT_ATOMS list. This is an integer serial number. Data items in the PDBX_DOMAIN category record information about domain definitions. A domain need not correspond to a completely polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain. Example 1 - <PDBx:pdbx_domainCategory> <PDBx:pdbx_domain id="d1"> <PDBx:details>Chains A, B</PDBx:details> </PDBx:pdbx_domain> <PDBx:pdbx_domain id="d2"> <PDBx:details>Asym_id D Residues 1-134</PDBx:details> </PDBx:pdbx_domain> </PDBx:pdbx_domainCategory> A description of special aspects of the structural elements that comprise a domain. The loop between residues 18 and 23. The value of attribute id in category pdbx_domain must uniquely identify a record in the PDBX_DOMAIN list. Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_DOMAIN_RANGE category identify the beginning and ending points of polypeptide chain segments that form all or part of a domain. Example 1 - <PDBx:pdbx_domain_rangeCategory> <PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="A" beg_label_comp_id="PRO" beg_label_seq_id="1" domain_id="d1" end_label_alt_id="A" end_label_asym_id="A" end_label_comp_id="GLY" end_label_seq_id="29"></PDBx:pdbx_domain_range> <PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="B" beg_label_comp_id="PRO" beg_label_seq_id="31" domain_id="d1" end_label_alt_id="A" end_label_asym_id="B" end_label_comp_id="GLY" end_label_seq_id="59"></PDBx:pdbx_domain_range> <PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="C" beg_label_comp_id="PRO" beg_label_seq_id="61" domain_id="d1" end_label_alt_id="A" end_label_asym_id="B" end_label_comp_id="GLY" end_label_seq_id="89"></PDBx:pdbx_domain_range> <PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="D" beg_label_comp_id="PRO" beg_label_seq_id="91" domain_id="d2" end_label_alt_id="A" end_label_asym_id="D" end_label_comp_id="GLY" end_label_seq_id="119"></PDBx:pdbx_domain_range> <PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="E" beg_label_comp_id="PRO" beg_label_seq_id="121" domain_id="d2" end_label_alt_id="A" end_label_asym_id="E" end_label_comp_id="GLY" end_label_seq_id="149"></PDBx:pdbx_domain_range> <PDBx:pdbx_domain_range beg_label_alt_id="A" beg_label_asym_id="F" beg_label_comp_id="PRO" beg_label_seq_id="151" domain_id="d2" end_label_alt_id="A" end_label_asym_id="F" end_label_comp_id="GLY" end_label_seq_id="179"></PDBx:pdbx_domain_range> </PDBx:pdbx_domain_rangeCategory> A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute id in category pdbx_domain in the PDBX_DOMAIN category. A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Data items in the PDBX_DRUG_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated. Example 1 - based on NDB entry DDH048 <PDBx:pdbx_drug_infoCategory> <PDBx:pdbx_drug_info id="1" name="ACTINOMYCIN D"> <PDBx:num_of_whole_molecule>2</PDBx:num_of_whole_molecule> <PDBx:num_per_asym_unit>2</PDBx:num_per_asym_unit> <PDBx:size_of_molecule_per_asym_unit>HALF</PDBx:size_of_molecule_per_asym_unit> </PDBx:pdbx_drug_info> </PDBx:pdbx_drug_infoCategory> Number of drug molecules per biological unit. Number of drug molecules per asymmetric unit. Size of drug molecules per asymmetric unit. half whole quarter Serial number. Common name of drug. The PDBX_ENTITY_ASSEMBLY category provides a chemical description of the biological assembly studied in terms of its constituent entities. A complex composed of one copy of entities 1 and 2. <PDBx:pdbx_entity_assemblyCategory> <PDBx:pdbx_entity_assembly entity_id="1" id="1"> <PDBx:biol_id>1</PDBx:biol_id> <PDBx:num_copies>1</PDBx:num_copies> </PDBx:pdbx_entity_assembly> <PDBx:pdbx_entity_assembly entity_id="2" id="1"> <PDBx:biol_id>1</PDBx:biol_id> <PDBx:num_copies>1</PDBx:num_copies> </PDBx:pdbx_entity_assembly> </PDBx:pdbx_entity_assemblyCategory> An identifier for the assembly. The number of copies of this entity in the assembly. An enity identifier. A reference to attribute id in category entity. An identifier for the assembly. Data items in the PDBX_ENTITY_BRANCH category specify the list of branched entities and the type. Example 1 - <PDBx:pdbx_entity_branchCategory> <PDBx:pdbx_entity_branch entity_id="2"> <PDBx:type>oligosaccharide</PDBx:type> </PDBx:pdbx_entity_branch> </PDBx:pdbx_entity_branchCategory> The type of this branched oligosaccharide. The entity id for this branched entity. This data item is a pointer to attribute id in category entity Data items in the PDBX_ENTITY_BRANCH_DESCRIPTOR category provide string descriptors of entity chemical structure. Example 1 - <PDBx:pdbx_entity_branch_descriptorCategory> <PDBx:pdbx_entity_branch_descriptor ordinal="1"> <PDBx:descriptor>[][Asn]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}</PDBx:descriptor> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:program>PDB-CARE</PDBx:program> <PDBx:program_version>Beta</PDBx:program_version> <PDBx:type>LINUCS</PDBx:type> </PDBx:pdbx_entity_branch_descriptor> </PDBx:pdbx_entity_branch_descriptorCategory> This data item contains the descriptor value for this entity. This data item is a pointer to attribute entity_id in category entity_poly in the ENTITY category. This data item contains the name of the program or library used to compute the descriptor. PDB-CARE Other program or library OTHER GEMS This data item contains the version of the program or library used to compute the descriptor. This data item contains the descriptor type. Ordinal index for this category. Data items in the PDBX_ENTITY_BRANCH_LINK category give details about the linkages between components within a branched entity. Example 1 - base on PDB entry 2WMG <PDBx:pdbx_entity_branch_linkCategory> <PDBx:pdbx_entity_branch_link link_id="1"> <PDBx:atom_id_1>O4</PDBx:atom_id_1> <PDBx:atom_id_2>C1</PDBx:atom_id_2> <PDBx:atom_stereo_config_2>R</PDBx:atom_stereo_config_2> <PDBx:comp_id_1>NAG</PDBx:comp_id_1> <PDBx:comp_id_2>GAL</PDBx:comp_id_2> <PDBx:entity_branch_list_num_1>1</PDBx:entity_branch_list_num_1> <PDBx:entity_branch_list_num_2>2</PDBx:entity_branch_list_num_2> <PDBx:entity_id>2</PDBx:entity_id> <PDBx:leaving_atom_id_1>HO4</PDBx:leaving_atom_id_1> <PDBx:leaving_atom_id_2>O1</PDBx:leaving_atom_id_2> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_entity_branch_link> <PDBx:pdbx_entity_branch_link link_id="2"> <PDBx:atom_id_1>O2</PDBx:atom_id_1> <PDBx:atom_id_2>C1</PDBx:atom_id_2> <PDBx:atom_stereo_config_2>R</PDBx:atom_stereo_config_2> <PDBx:comp_id_1>GAL</PDBx:comp_id_1> <PDBx:comp_id_2>FUC</PDBx:comp_id_2> <PDBx:entity_branch_list_num_1>2</PDBx:entity_branch_list_num_1> <PDBx:entity_branch_list_num_2>3</PDBx:entity_branch_list_num_2> <PDBx:entity_id>2</PDBx:entity_id> <PDBx:leaving_atom_id_1>HO2</PDBx:leaving_atom_id_1> <PDBx:leaving_atom_id_2>O1</PDBx:leaving_atom_id_2> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_entity_branch_link> <PDBx:pdbx_entity_branch_link link_id="3"> <PDBx:atom_id_1>O3</PDBx:atom_id_1> <PDBx:atom_id_2>C1</PDBx:atom_id_2> <PDBx:atom_stereo_config_2>R</PDBx:atom_stereo_config_2> <PDBx:comp_id_1>NAG</PDBx:comp_id_1> <PDBx:comp_id_2>FUC</PDBx:comp_id_2> <PDBx:entity_branch_list_num_1>1</PDBx:entity_branch_list_num_1> <PDBx:entity_branch_list_num_2>4</PDBx:entity_branch_list_num_2> <PDBx:entity_id>2</PDBx:entity_id> <PDBx:leaving_atom_id_1>HO3</PDBx:leaving_atom_id_1> <PDBx:leaving_atom_id_2>O1</PDBx:leaving_atom_id_2> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_entity_branch_link> </PDBx:pdbx_entity_branch_linkCategory> The atom identifier/name for the first atom making the linkage. The atom identifier/name for the second atom making the linkage. The chiral configuration of the first atom making the linkage. The chiral configuration of the second atom making the linkage. The component identifier for the first component making the linkage. This data item is a pointer to attribute comp_id in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. The component identifier for the second component making the linkage. This data item is a pointer to attribute comp_id in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. A description of special aspects of this linkage. The component number for the first component making the linkage. This data item is a pointer to attribute num in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. The component number for the second component making the linkage. This data item is a pointer to attribute num in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. The entity id for this branched entity. This data item is a pointer to attribute entity_id in category pdbx_entity_branch_list in the PDBX_ENTITY_BRANCH_LIST category. The leaving atom identifier/name bonded to the first atom making the linkage. The leaving atom identifier/name bonded to the second atom making the linkage. The bond order target for the chemical linkage. The value of attribute link_id in category pdbx_entity_branch_link uniquely identifies linkages within the branched entity. Data items in the PDBX_ENTITY_BRANCH_LIST category specify the list of monomers in a branched entity. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity. Example 1 - <PDBx:pdbx_entity_branch_listCategory> <PDBx:pdbx_entity_branch_list comp_id="NAG" entity_id="2" num="1"> <PDBx:hetero>n</PDBx:hetero> </PDBx:pdbx_entity_branch_list> <PDBx:pdbx_entity_branch_list comp_id="GAL" entity_id="2" num="2"> <PDBx:hetero>n</PDBx:hetero> </PDBx:pdbx_entity_branch_list> <PDBx:pdbx_entity_branch_list comp_id="FUC" entity_id="2" num="3"> <PDBx:hetero>n</PDBx:hetero> </PDBx:pdbx_entity_branch_list> <PDBx:pdbx_entity_branch_list comp_id="FUC" entity_id="2" num="4"> <PDBx:hetero>n</PDBx:hetero> </PDBx:pdbx_entity_branch_list> </PDBx:pdbx_entity_branch_listCategory> A flag to indicate whether this monomer in the entity is heterogeneous in sequence. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. This data item is a pointer to attribute id in category entity in the ENTITY category. The value pair _pdbx_entity_branch_list.num and _pdbx_entity_branch_list.comp_id must uniquely identify a record in the PDBX_ENTITY_BRANCH_LIST list. Data items in the PDBX_ENTITY_FUNC_BIND_MODE category describe characteristics of protein oligonucleotide binding. This data item identifies the type of oligonucleotide to which the protein binds. This data item describes the functional type of the protein oligonucleotide binding interaction. This data item is a pointer to attribute id in category pdbx_entity_poly_domain in the PDBX_ENTITY_POLY_DOMAIN category. This data item is a pointer to attribute id in category entity in the ENTITY category. The value of attribute id in category pdbx_entity_func_bind_mode is a unique identifier for a binding mode within a domain within an entity. Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_ENTITY_FUNC_ENZYME category describe characteristics of protein oligonucleotide binding in which the binding mode is enzymatic. This data item describes the type of enzyme function. This data item is pointer to attribute id in category pdbx_entity_func_bind_mode in the PDBX_ENTITY_FUNC_BIND_MODE category. Data items in the PDBX_ENTITY_FUNC_OTHER category describe characteristics of protein oligonucleotide binding in which the binding mode is not classified. This data item describes the type of structural function. This data item is pointer to attribute id in category pdbx_entity_func_bind_mode in the PDBX_ENTITY_FUNC_BIND_MODE category. Data items in the PDBX_ENTITY_FUNC_REGULATORY category describe characteristics of protein oligonucleotide binding in which the binding mode is regulatory. This data item describes the type of regulatory function. This data item is pointer to attribute id in category pdbx_entity_func_bind_mode in the PDBX_ENTITY_FUNC_BIND_MODE category. Data items in the PDBX_ENTITY_FUNC_STRUCTURAL category describe characteristics of protein oligonucleotide binding in which the binding mode is structural. This data item describes the type of structural function. This data item is pointer to attribute id in category pdbx_entity_func_bind_mode in the PDBX_ENTITY_FUNC_BIND_MODE category. Data items in the pdbx_entity_instance_feature category records special features of selected entity instances. Example 1 - <PDBx:pdbx_entity_instance_featureCategory> <PDBx:pdbx_entity_instance_feature ordinal="1"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>R77</PDBx:auth_comp_id> <PDBx:auth_seq_num>47</PDBx:auth_seq_num> <PDBx:comp_id>Q20</PDBx:comp_id> <PDBx:feature_type>SUBJECT OF INVESTIGATION</PDBx:feature_type> </PDBx:pdbx_entity_instance_feature> </PDBx:pdbx_entity_instance_featureCategory> Instance identifier for this entity. A B Author instance identifier (formerly PDB Chain ID) A B The author provided chemical component identifier NAG ATP Author provided residue number. 1 2 Chemical component identifier NAG ATP Special structural details about this entity instance. A feature type associated with entity instance. Position in the sequence. 1 2 An ordinal index for this category 1 2 The PDBX_ENTITY_NAME records additional name information for each entity. Example 1 - <PDBx:pdbx_entity_nameCategory> <PDBx:pdbx_entity_name entity_id="1" name="PLASTOCYANIN" name_type="SWS-NAME"></PDBx:pdbx_entity_name> <PDBx:pdbx_entity_name entity_id="1" name="Electron transport" name_type="SWS-KEYWORD"></PDBx:pdbx_entity_name> </PDBx:pdbx_entity_nameCategory> Pointer to attribute id in category entity. Entity name. Entity name type. Data items in the PDBX_ENTITY_NAME_INSTANCE category list names used to define entities with their associated database, entity, chain, and molecule identifiers. <PDBx:pdbx_entity_name_instanceCategory> <PDBx:pdbx_entity_name_instance entity_id="1" name="ALCOHOL DEHYDROGENASE" pdb_id="1B2L"> <PDBx:pdb_chain_id>A</PDBx:pdb_chain_id> <PDBx:pdb_mol_id>1</PDBx:pdb_mol_id> <PDBx:rcsb_id>RCSB000146</PDBx:rcsb_id> </PDBx:pdbx_entity_name_instance> </PDBx:pdbx_entity_name_instanceCategory> This data item holds the PDB chain id of this entity within the entry. This data item holds the PDB molecule id of this entity within the entry. This data item holds a RCSB ID code. This data item holds the entity_id of this entity within the entry. This data item holds an entity name. This data item holds a PDB ID code Data items in the PDBX_ENTITY_NAME_TAXONOMY category define the names and synonyms of the entity name taxonomy. <PDBx:pdbx_entity_name_taxonomyCategory> <PDBx:pdbx_entity_name_taxonomy id="alcohol dehydrogenase" name="alcohol dehydrogenase"> <PDBx:name_type>STANDARD</PDBx:name_type> </PDBx:pdbx_entity_name_taxonomy> <PDBx:pdbx_entity_name_taxonomy id="alcohol dehydrogenase" name="adhg"> <PDBx:name_type>SYNONYM</PDBx:name_type> </PDBx:pdbx_entity_name_taxonomy> <PDBx:pdbx_entity_name_taxonomy id="alcohol dehydrogenase" name="steroid active alcohol dehydrogenase"> <PDBx:name_type>SUBCLASS</PDBx:name_type> </PDBx:pdbx_entity_name_taxonomy> <PDBx:pdbx_entity_name_taxonomy id="alcohol dehydrogenase" name="$ALCOHOL DEHYDROGENASE$"> <PDBx:name_type>DEPRECATED</PDBx:name_type> </PDBx:pdbx_entity_name_taxonomy> </PDBx:pdbx_entity_name_taxonomyCategory> This data item classifies the entity name within a taxonomic node. This data item holds an node identifier in the entity name taxonomy tree. This data item holds an entity name or synonym. Data items in the PDBX_ENTITY_NAME_TAXONOMY_TREE category define the tree structure of the entity name taxonomy. <PDBx:pdbx_entity_name_taxonomy_treeCategory> <PDBx:pdbx_entity_name_taxonomy_tree id="Oxidoreductases" parent_id="-"></PDBx:pdbx_entity_name_taxonomy_tree> <PDBx:pdbx_entity_name_taxonomy_tree id="alcohol dehydrogenase" parent_id="Oxidoreductases"></PDBx:pdbx_entity_name_taxonomy_tree> <PDBx:pdbx_entity_name_taxonomy_tree id="alcohol dehydrogenase (NADP)" parent_id="Oxidoreductases"></PDBx:pdbx_entity_name_taxonomy_tree> <PDBx:pdbx_entity_name_taxonomy_tree id="homoserine dehydrogenase" parent_id="Oxidoreductases"></PDBx:pdbx_entity_name_taxonomy_tree> <PDBx:pdbx_entity_name_taxonomy_tree id="Transferases" parent_id="-"></PDBx:pdbx_entity_name_taxonomy_tree> <PDBx:pdbx_entity_name_taxonomy_tree id="nicotinamide N-methyltransferase" parent_id="Transferases"></PDBx:pdbx_entity_name_taxonomy_tree> <PDBx:pdbx_entity_name_taxonomy_tree id="glycine N-methyltransferase" parent_id="Transferases"></PDBx:pdbx_entity_name_taxonomy_tree> </PDBx:pdbx_entity_name_taxonomy_treeCategory> This data item identifies a node in the entity name taxonomy. This data item identifies the nearest parent node in the entity name taxonomy. The PDBX_ENTITY_NONPOLY category provides a mapping between entity and the nonpolymer component Example 1 - This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. A name for the non-polymer entity This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the PDBX_ENTITY_POLY_COMP_LINK_LIST category enumerate the linkages between components within the polymer entity. Example 1 - <PDBx:pdbx_entity_poly_comp_link_listCategory> <PDBx:pdbx_entity_poly_comp_link_list link_id="1"> <PDBx:atom_id_1 xsi:nil="true" /> <PDBx:atom_id_2 xsi:nil="true" /> <PDBx:atom_stereo_config_1 xsi:nil="true" /> <PDBx:atom_stereo_config_2 xsi:nil="true" /> <PDBx:comp_id_1 xsi:nil="true" /> <PDBx:comp_id_2 xsi:nil="true" /> <PDBx:entity_comp_num_1>1</PDBx:entity_comp_num_1> <PDBx:entity_comp_num_2>2</PDBx:entity_comp_num_2> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:leaving_atom_id_1 xsi:nil="true" /> <PDBx:leaving_atom_id_2 xsi:nil="true" /> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_entity_poly_comp_link_list> </PDBx:pdbx_entity_poly_comp_link_listCategory> The atom identifier/name for the first atom making the linkage. The atom identifier/name for the second atom making the linkage. The chiral configuration of the first atom making the linkage. The chiral configuration of the second atom making the linkage. The component identifier for the first component making the linkage. This data item is a pointer to attribute mon_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. The component identifier for the second component making the linkage. This data item is a pointer to attribute mon_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. A description of special aspects of this linkage. The component number for the first component making the linkage. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. The component number for the second component making the linkage. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. The entity id for this branched entity. This data item is a pointer to attribute entity_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. The leaving atom identifier/name bonded to the first atom making the linkage. The leaving atom identifier/name bonded to the second atom making the linkage. The bond order target for the chemical linkage. The value of attribute link_id in category pdbx_entity_poly_comp_link_list uniquely identifies linkages within the branched entity. Data items in the PDBX_ENTITY_POLY_DOMAIN category specify domains of monomers within a polymer. The value of attribute begin_mon_id in category pdbx_entity_poly_domain identifies the monomer at the beginning of the domain. This must correspond to a record in the ENTITY_POLY_SEQ list. The value of attribute begin_seq_num in category pdbx_entity_poly_domain identifies the sequence position of the beginning of the domain. This must correspond to a record in the ENTITY_POLY_SEQ list. The value of attribute begin_mon_id in category pdbx_entity_poly_domain identifies the monomer at the end of the domain. This must correspond to a record in the ENTITY_POLY_SEQ list. The value of attribute begin_seq_num in category pdbx_entity_poly_domain identifies the sequence position of the end of the domain. This must correspond to a record in the ENTITY_POLY_SEQ list. This data item is a pointer to attribute id in category entity in the ENTITY category. The value of attribute id in category pdbx_entity_poly_domain must uniquely identify a domain within an entity. Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_ENTITY_POLY_NA_NONSTANDARD category describe the nonstandard features of the nucleic acid polymer entities. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item describes the nonstandard feature of the nucleic acid polymer entity. Data items in the PDBX_ENTITY_POLY_NA_TYPE category describe type of nucleic acid polymer entities. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item describes the nucleic acid type. Data items in the PDBX_ENTITY_POLY_PROTEIN_CLASS category provides a top-level protein classification. This data item provides a top-level classification of the polymer protein entity. This data item is a pointer to attribute id in category entity in the ENTITY category. This category contains descriptive protocols for the production of this entity. The protocol description associated with the protocol_type employed in the production of this entity. The value of attribute entity_id in category pdbx_entity_prod_protocol uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. The value of attribute entry_id in category pdbx_entity_prod_protocol uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. The one of a set of protocol types associated with the production of this entity. This category contains details of protein characterisation. It refers to the characteristion of the product of a specific step. The date of characterisation step. 2003-12-25 2003-12-25:09:00 Any details associated with this method of protein characterisation. The method used for protein characterisation. Dynamic light scattering Mass spectrometry The result from this method of protein characterisation. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The value of attribute entity_id in category pdbx_entity_src_gen_character uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_character uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for the step whose product has been characterised. This category contains details for the chromatographic steps used in the purification of the protein. The temperature in degrees celsius at which this column was run. The type of column used in this step. The volume of the column used in this step. The date of production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that with which the protein was eluted. Details of the elution protocol. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the chromatography step. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the column was equilibrated. The rate at which the equilibration buffer flowed through the column. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. Details of any post-chromatographic treatment of the protein sample. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The method used to determine the concentration of the protein solution put onto the column. The concentration of the protein solution put onto the column. Details of the sample preparation prior to running the column. The volume of protein solution run on the column. The total volume of all the fractions pooled to give the purified protein solution. The method used to determine the yield The yield in milligrams of protein recovered in the pooled fractions. The value of attribute entity_id in category pdbx_entity_src_gen_chrom uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_chrom uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this chromatography step. This category contains details for the cloning steps used in the overall protein production process. Each row in PDBX_ENTITY_SRC_GEN_CLONE should have an equivalent row in either PDBX_ENTITY_SRC_GEN_CLONE_LIGATION or PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION. If only summary information is provided data in the later two categories may be omitted. The date of this production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the cloned product. The method used to insert the gene into the vector. For 'Ligation', an PDBX_ENTITY_SRC_GEN_CLONE_LIGATION entry with matching .step_id is expected. For 'Recombination', an PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION entry with matching .step_id is expected. The type of marker included to allow selection of transformed cells This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. Details of any purification of the product. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. Summary of ligation or recombionation cloning used, the associated verification method and any purification of the product. The method used to transform the expression cell line with the vector Details of any modifications made to the named vector. The name of the vector used in this cloning step. The method used to verify that the incorporated gene is correct The value of attribute entity_id in category pdbx_entity_src_gen_clone uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_clone uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this cloning step. This category contains details for the ligation-based cloning steps used in the overall protein production process. attribute clone_step_id in category pdbx_entity_src_gen_clone_ligation in this category must point at a defined attribute step_id in category pdbx_entity_src_gen_clone. The details in PDBX_ENTITY_SRC_GEN_CLONE_LIGATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover ligation dependent cloning steps. The names of the enzymes used to cleave the vector. In addition an enzyme used to blunt the cut ends, etc., should be named here. Any details to be associated with this ligation step, e.g. the protocol. The names of the enzymes used to ligate the gene into the cleaved vector. The temperature at which the ligation experiment was performed, in degrees celsius. The duration of the ligation reaction in minutes. This item is a pointer to attribute entity_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This item is a pointer to attribute entry_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This item is a pointer to attribute step_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This category contains details for the recombination-based cloning steps used in the overall protein production process. It is assumed that these reactions will use commercially available kits. attribute clone_step_id in category pdbx_entity_src_gen_clone_recombination in this category must point at a defined attribute step_id in category pdbx_entity_src_gen_clone. The details in PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover recombination dependent cloning steps. Any details to be associated with this recombination step, e.g. the protocol or differences from the manufacturer's specified protocol. The names of the enzymes used for this recombination step. The name of the recombination system. This item is a pointer to attribute entity_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This item is a pointer to attribute entry_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. This item is a pointer to attribute step_id in category pdbx_entity_src_gen_clone in the PDBX_ENTITY_SRC_GEN_CLONE category. Data items in the PDBX_ENTITY_SRC_GEN_DEPOSITOR_INFO category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid). Example - Fusion protein case- 3L2J Fusion protein of maltose-binding periplasmic protein and parathyroid hormone/parathyroid hormone-related peptide receptor. <PDBx:pdbx_entity_src_gen_depositor_infoCategory> <PDBx:pdbx_entity_src_gen_depositor_info src_id="1"> <PDBx:beg_seq_num>1</PDBx:beg_seq_num> <PDBx:end_seq_num>364</PDBx:end_seq_num> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:gene_src_gene>b4034, JW3994</PDBx:gene_src_gene> <PDBx:gene_src_ncbi_taxonomy_id>83333</PDBx:gene_src_ncbi_taxonomy_id> <PDBx:gene_src_scientific_name>Escherichia coli</PDBx:gene_src_scientific_name> <PDBx:host_org_ncbi_taxonomy_id>562</PDBx:host_org_ncbi_taxonomy_id> <PDBx:host_org_scientific_name>Escherichia coli</PDBx:host_org_scientific_name> <PDBx:host_org_vector_type>plasmid</PDBx:host_org_vector_type> <PDBx:plasmid_name>pGEX6p-2RBS</PDBx:plasmid_name> </PDBx:pdbx_entity_src_gen_depositor_info> <PDBx:pdbx_entity_src_gen_depositor_info src_id="2"> <PDBx:beg_seq_num>365</PDBx:beg_seq_num> <PDBx:end_seq_num>370</PDBx:end_seq_num> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:gene_src_ncbi_taxonomy_id>32630</PDBx:gene_src_ncbi_taxonomy_id> <PDBx:gene_src_scientific_name>synthetic construct</PDBx:gene_src_scientific_name> <PDBx:host_org_ncbi_taxonomy_id>562</PDBx:host_org_ncbi_taxonomy_id> <PDBx:host_org_scientific_name>Escherichia coli</PDBx:host_org_scientific_name> <PDBx:host_org_vector_type>plasmid</PDBx:host_org_vector_type> <PDBx:plasmid_name>pGEX6p-2RBS</PDBx:plasmid_name> </PDBx:pdbx_entity_src_gen_depositor_info> <PDBx:pdbx_entity_src_gen_depositor_info src_id="3"> <PDBx:beg_seq_num>371</PDBx:beg_seq_num> <PDBx:end_seq_num>529</PDBx:end_seq_num> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:gene_src_gene>malE, PTHR1</PDBx:gene_src_gene> <PDBx:gene_src_ncbi_taxonomy_id>9606</PDBx:gene_src_ncbi_taxonomy_id> <PDBx:gene_src_scientific_name>Homo sapiens</PDBx:gene_src_scientific_name> <PDBx:host_org_ncbi_taxonomy_id>562</PDBx:host_org_ncbi_taxonomy_id> <PDBx:host_org_scientific_name>Escherichia coli</PDBx:host_org_scientific_name> <PDBx:host_org_vector_type>plasmid</PDBx:host_org_vector_type> <PDBx:plasmid_name>pGEX6p-2RBS</PDBx:plasmid_name> </PDBx:pdbx_entity_src_gen_depositor_info> <PDBx:pdbx_entity_src_gen_depositor_info src_id="4"> <PDBx:beg_seq_num>530</PDBx:beg_seq_num> <PDBx:end_seq_num>535</PDBx:end_seq_num> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:gene_src_ncbi_taxonomy_id>32630</PDBx:gene_src_ncbi_taxonomy_id> <PDBx:gene_src_scientific_name>synthetic construct</PDBx:gene_src_scientific_name> <PDBx:host_org_ncbi_taxonomy_id>562</PDBx:host_org_ncbi_taxonomy_id> <PDBx:host_org_scientific_name>Escherichia coli</PDBx:host_org_scientific_name> <PDBx:host_org_vector_type>plasmid</PDBx:host_org_vector_type> <PDBx:plasmid_name>pGEX6p-2RBS</PDBx:plasmid_name> </PDBx:pdbx_entity_src_gen_depositor_info> </PDBx:pdbx_entity_src_gen_depositor_infoCategory> The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. The entity id for this chimeric entity. This data item is a pointer to attribute entity_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. Identifies the gene. NCBI Taxonomy identifier for the gene source organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. Scientific name of the organism. ESCHERICHIA COLI HOMO SAPIENS SACCHAROMYCES CEREVISIAE Specific gene which expressed the molecule. HIV-1 POL GLNS7 U1A (2-98, Y31H, Q36R) NCBI Taxonomy identifier for the expression system organism. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. The scientific name of the organism that served as host for the production of the entity. Where full details of the protein production are available it would be expected that this item would be derived from attribute host_org_scientific_name in category entity_src_gen_express or via attribute host_org_tax_id in category entity_src_gen_express ESCHERICHIA COLI SACCHAROMYCES CEREVISIAE The strain of the organism in which the entity was expressed. AR120 Identifies the type of vector used (plasmid, virus, or cosmid). Where full details of the protein production are available it would be expected that this item would be derived from attribute vector_type in category entity_src_gen_express. COSMID PLASMID The name of the plasmid that produced the entity in the host organism. Where full details of the protein production are available it would be expected that this item would be derived from attribute name in category pdbx_construct of the construct pointed to from attribute plasmid_id in category entity_src_gen_express. pET3C pT123sab This data item povides additional information about the sequence type. This data item is an ordinal identifier for entity_src_gen data records. This category contains details for the EXPRESSION steps used in the overall protein production process. It is hoped that this category will cover all forms of cell-based expression by reading induction as induction/transformation/transfection. Any C-terminal sequence tag as a string of one letter amino acid codes Any N-terminal sequence tag as a string of one letter amino acid codes. Any additives to the base media in which the expression host was grown. The name of the base media in which the expression host was grown. The temperature in degrees celsius at which the expression host was allowed to grow prior to induction/transformation/transfection. The time in hours for which the expression host was allowed to grow prior to induction/transformation/transfection. The volume of media in milliliters in which the expression host was grown. The date of production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product. Details of the harvesting protocol. A specific line of cells used as the expression system The common name of the organism that served as host for the expression system. Where attribute host_org_tax_id in category pdbx_entity_src_gen_express is populated it is expected that this item may be derived by look up against the taxonomy database. Culture collection of the expression system A description of special aspects of the organism that served as host for the expression system. The scientific name of the organism that served as host for the expression system. It is expected that either this item or attribute host_org_tax_id in category pdbx_entity_src_gen_express should be populated. The strain of the organism that served as host for the expression system. Where attribute host_org_tax_id in category pdbx_entity_src_gen_express is populated it is expected that this item may be derived by a look up against the taxonomy database. The id for the NCBI taxonomy node corresponding to the organism that served as host for the expression system. The specific tissue which expressed the molecule. The vairant of the organism that served as host for the expression system. Where attribute host_org_tax_id in category pdbx_entity_src_gen_express is populated it is expected that this item may be derived by a look up against the taxonomy database. The chemical name of the inducing agent. Concentration of the inducing agent. Details of induction/transformation/transfection. The temperature in celsius at which the induced/transformed/transfected cells were grown. The time in hours after induction/transformation/transfection at which the optical density of the culture was measured. The multiplicity of infection for genes introduced by transfection, eg. for baculovirus-based expression. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. This item is a pointer to attribute id in category pdbx_construct in the PDBX_CONSTRUCT category. The referenced entry will contain the nucleotide sequence that is to be expressed, including tags. The nature of the promoter controlling expression of the gene. T7 LacZ This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. Details of how the harvested culture was stored. Summary of the details of the expression steps used in protein production. Identifies the type of vector used (plasmid, virus, or cosmid) in the expression system. The value of attribute entity_id in category pdbx_entity_src_gen_express uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_express uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this expression step. This category contains details for OD time series used to monitor a given EXPRESSION step used in the overall protein production process. The optical density of the expression culture in arbitrary units at the timepoint specified. The time in hours after induction/transformation/transfection at which the optical density of the culture was measured. The value of attribute entity_id in category pdbx_entity_src_gen_express_timepoint is a pointer to attribute entity_id in category pdbx_entity_src_gen_express The value of attribute entry_id in category pdbx_entity_src_gen_express_timepoint is a pointer to attribute entry_id in category pdbx_entity_src_gen_express This items uniquely defines a timepoint within a series. This item is a pointer to attribute step_id in category pdbx_entity_src_gen_express This category contains details for the fraction steps used in the overall protein production process. Examples of fractionation steps are centrifugation and magnetic bead pull-down purification. The date of this production step. 2003-12-25 2003-12-25:09:00 String value containing details of the fractionation. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the fractionation step. This item describes the method of fractionation. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. The fraction containing the protein of interest. The volume of the fraction containing the protein. The yield in milligrams of protein from the fractionation. The method used to determine the yield This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The temperature in degrees celsius at which the fractionation was performed. The value of attribute entity_id in category pdbx_entity_src_gen_fract uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_fract uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this fractionation step. This category contains details for the cell lysis steps used in the overall protein production process. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the lysis was performed. The volume in milliliters of buffer in which the lysis was performed. The date of this production step. 2003-12-25 2003-12-25:09:00 String value containing details of the lysis protocol. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after lysis. The lysis method. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The temperature in degrees celsius at which the lysis was performed. The time in seconds of the lysis experiment. The value of attribute entity_id in category pdbx_entity_src_gen_lysis uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_lysis uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this lysis step. This category contains details for the DIGEST steps used in the overall protein production process. The digestion is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step. Example 1 - hypothetical example <PDBx:pdbx_entity_src_gen_prod_digestCategory> <PDBx:pdbx_entity_src_gen_prod_digest entity_id="222000111" entry_id="111000111" step_id="2"> <PDBx:date>2002-07-12:15:13</PDBx:date> <PDBx:end_construct_id>440050000123</PDBx:end_construct_id> <PDBx:next_step_id>3</PDBx:next_step_id> <PDBx:purification_details> No purification</PDBx:purification_details> <PDBx:restriction_enzyme_1>NcoI</PDBx:restriction_enzyme_1> <PDBx:restriction_enzyme_2>BamII</PDBx:restriction_enzyme_2> <PDBx:robot_id>5</PDBx:robot_id> </PDBx:pdbx_entity_src_gen_prod_digest> </PDBx:pdbx_entity_src_gen_prod_digestCategory> The date of this production step. 2003-12-25 This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the digest product This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. String value containing details of any purification of the product of the digestion. The first enzyme used in the restriction digestion. The sites at which this cuts can be derived from the sequence. BamIII The second enzyme used in the restriction digestion. The sites at which this cuts can be derived from the sequence. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. Summary of the details of restriction digestion any purification of the product of the digestion. The value of attribute entity_id in category pdbx_entity_src_gen_prod_digest uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_prod_digest uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this digestion step. This category contains details for process steps that are not explicitly catered for elsewhere. It provides some basic details as well as placeholders for a list of parameters and values (the category PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER). Note that processes that have been modelled explicitly should not be represented using this category. The date of this process step. 2003-12-25 2003-12-25:09:00 Additional details of this process step. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the product of the process step. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. Name of this process step. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The referenced robot is the robot responsible for the process step The value of attribute entity_id in category pdbx_entity_src_gen_prod_other uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_prod_other uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this process step. This category contains parameters and values required to capture information about a particular process step Additional details about the parameter The value of the parameter The value of attribute entity_id in category pdbx_entity_src_gen_prod_other_parameter is a pointer to attribute entity_id in category pdbx_entity_src_gen_prod_other The value of attribute entry_id in category pdbx_entity_src_gen_prod_other_parameter is a pointer to attribute entry.id in category pdbx_entity_src_gen_prod_other The name of the parameter associated with the process step This item is a pointer to attribute step_id in category pdbx_entity_src_gen_prod_other This category contains details for the PCR steps used in the overall protein production process. The PCR is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step. Example 1 - hypothetical example <PDBx:pdbx_entity_src_gen_prod_pcrCategory> <PDBx:pdbx_entity_src_gen_prod_pcr entity_id="222000111" entry_id="111000111" step_id="1"> <PDBx:date>2002-07-12:15:13</PDBx:date> <PDBx:end_construct_id>440050000111</PDBx:end_construct_id> <PDBx:forward_primer_id>2</PDBx:forward_primer_id> <PDBx:next_step_id>2</PDBx:next_step_id> <PDBx:purification_details> No purification</PDBx:purification_details> <PDBx:reaction_details> Annealing temperature = 70 C Annealing time = 60 s Extending temperature = 74 C Extending time = 120 s Melting temperature = 95 C Melting time = 120 s Number of cycles = 40 Polymerase = KOD Template = 10 pmol Primer = 25 pmol Total volume = 25 ul</PDBx:reaction_details> <PDBx:reverse_primer_id>3</PDBx:reverse_primer_id> <PDBx:robot_id>5</PDBx:robot_id> </PDBx:pdbx_entity_src_gen_prod_pcr> </PDBx:pdbx_entity_src_gen_prod_pcrCategory> The date of this production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the PCR product. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the forward primer. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. String value containing details of any purification of the product of the PCR reaction. String value containing details of the PCR reaction. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced nucleic acid sequence is that of the reverse primer. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The referenced robot is the robot responsible for the PCR reaction (normally the heat cycler). Summary of the details of the PCR reaction any purification of the product of the PCR reaction. The value of attribute entity_id in category pdbx_entity_src_gen_prod_pcr uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_prod_pcr uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this PCR step. This category contains details for the protein purification tag removal steps used in the overall protein production process This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the cleavage was performed. The temperature in degrees celsius at which the cleavage was performed. The time in minutes for the cleavage reaction The date of production step. 2003-12-25 2003-12-25:09:00 Details of this tag removal step. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the proteolysis step. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. The name of the protease used for cleavage. The ratio of protein to protease used for the cleavage. = mol protein / mol protease This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The value of attribute entity_id in category pdbx_entity_src_gen_proteolysis uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_proteolysis uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this tag removal step. This category contains details for the final purified protein product. Note that this category does not contain the amino acid sequence of the protein. The sequence will be found in the ENTITY_POLY_SEQ entry with matching entity_id. Only one PDBX_ENTITY_SRC_GEN_PURE category is allowed per entity, hence there is no step_id for this category. The method used to measure the protein concentration Details of the protein concentration procedure This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. The date of production step. 2003-12-25 2003-12-25:09:00 When present, this item should be a globally unique identifier that identifies the final product. It is envisaged that this should be the same as and product code associated with the sample and would provide the key by which information about the production process may be extracted from the protein production facility. For files describing the protein production process (i.e. where attribute type in category entity is 'P' or 'E') this should have the same value as attribute id in category entry The final concentration of the protein. The oligomeric state of the protein. Monomeric is 1, dimeric 2, etc. The purity of the protein (percent). The yield of protein in milligrams. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was stored. The temperature in degrees celsius at which the protein was stored. Summary of the details of protein purification method used to obtain the final protein product. This description should include any lysis, fractionation, proteolysis, refolding, chromatography used as well as the method used the characterize the final product. The value of attribute entity_id in category pdbx_entity_src_gen_pure uniquely identifies each protein contained in the project target complex proteins whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_pure uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item unique identifier the production step. This category contains details for the refolding steps used in the overall protein production process. The date of this production step. 2003-12-25 2003-12-25:09:00 This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was denatured. String value containing details of the refolding. This item is a pointer to pdbx_construct.id in the PDBX_CONSTRUCT category. The referenced sequence is expected to be the amino acid sequence of the expressed product after the refolding step. This item unique identifier for the next production step. This allows a workflow to have multiple entry points leading to a single product. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the protein was refolded. This data item is a pointer to pdbx_robot_system.id in the PDBX_ROBOT_SYSTEM category. This item is a pointer to pdbx_buffer.id in the PDBX_BUFFER category. The referenced buffer is that in which the refolded protein was stored. The temperature in degrees celsius at which the protein was refolded. The time in hours over which the protein was refolded. The value of attribute entity_id in category pdbx_entity_src_gen_refold uniquely identifies each protein contained in the project target protein complex whose structure is to be determined. This data item is a pointer to attribute id in category entity in the ENTITY category. This item may be a site dependent bar code. The value of attribute entry_id in category pdbx_entity_src_gen_refold uniquely identifies a sample consisting of one or more proteins whose structure is to be determined. This is a pointer to attribute id in category entry. This item may be a site dependent bar code. This item is the unique identifier for this refolding step. The data items in category PDBX_ENTITY_SRC_SYN record the source details about chemically synthesized molecules. A description of special aspects of the source for the synthetic entity. This sequence occurs naturally in humans. NCBI Taxonomy identifier of the organism from which the sequence of the synthetic entity was derived. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1;28(1):10-4 Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000). GenBank. Nucleic Acids Res 2000 Jan 1;28(1):15-18. The common name of the organism from which the sequence of the synthetic entity was derived. house mouse The scientific name of the organism from which the sequence of the synthetic entity was derived. Mus musculus This data item identifies cases in which an alternative source modeled. The beginning polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. The ending polymer sequence position for the polymer section corresponding to this source. A reference to the sequence position in the entity_poly category. The strain of the organism from which the sequence of the synthetic entity was derived. This data item is a pointer to attribute id in category entity in the ENTITY category. 1 2 3 4 This data item is an ordinal identifier for pdbx_entity_src_syn data records. Data items in the PDBX_ENTRY_DETAILS category provide additional details about this entry. Example 1 <PDBx:pdbx_entry_detailsCategory> <PDBx:pdbx_entry_details entry_id="1ABC"> <PDBx:nonpolymer_details>Inhibitor VX4A in this entry adopts a highly strained conformation about C32 inorder to fit into the cleft about the active site.</PDBx:nonpolymer_details> </PDBx:pdbx_entry_details> </PDBx:pdbx_entry_detailsCategory> Additional details about the macromolecular compounds in this entry. A flag to indicate if author has indicated that there are any or no ligands that are the focus of research. Y Additional details about the non-polymer components in this entry. Additional details about the sequence or sequence database correspondences for this entry. Additional details about the source and taxonomy of the macromolecular components in this entry. This item identifies the entry. This is a reference to attribute id in category entry. Data items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category record details cryogenic treatments applied to this crystal. Example 1 <PDBx:pdbx_exptl_crystal_cryo_treatmentCategory> <PDBx:pdbx_exptl_crystal_cryo_treatment crystal_id="4"> <PDBx:cooling_details> Direct immersion in liquid nitrogen</PDBx:cooling_details> <PDBx:final_solution_details> 25&#37; (v/v) glycerol in precipitant solution</PDBx:final_solution_details> <PDBx:soaking_details> A series of 1 min soaks beginning at 5&#37; (v/v) glycerol in precipitant, transiting to 20&#37; (v/v) glycerol, and finally to 25&#37; glycerol</PDBx:soaking_details> </PDBx:pdbx_exptl_crystal_cryo_treatment> </PDBx:pdbx_exptl_crystal_cryo_treatmentCategory> Details of the annealing treatment applied to this crystal. 10 sec interruption of cold stream with plastic ruler. Performed twice. Details of the cooling treatment applied to this crystal. Direct immersion in liquid nitrogen Details of the final solution used in the treatment of this crystal 25% (v/v) glycerol in precipitant solution Details of the soaking treatment applied to this crystal. A series of 1 min soaks beginning at 5% (v/v) glycerol in precipitant, transiting to 20% (v/v) glycerol, and finally to 25% glycerol This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' to produce the crystal. Example 1 - <PDBx:pdbx_exptl_crystal_grow_compCategory> <PDBx:pdbx_exptl_crystal_grow_comp comp_id="1" crystal_id="4"> <PDBx:comp_name>protein</PDBx:comp_name> <PDBx:conc>25.</PDBx:conc> <PDBx:conc_range xsi:nil="true" /> <PDBx:conc_units>mg/ml</PDBx:conc_units> <PDBx:sol_id>protein</PDBx:sol_id> </PDBx:pdbx_exptl_crystal_grow_comp> <PDBx:pdbx_exptl_crystal_grow_comp comp_id="2" crystal_id="4"> <PDBx:comp_name>Tris HCl</PDBx:comp_name> <PDBx:conc>20.</PDBx:conc> <PDBx:conc_range xsi:nil="true" /> <PDBx:conc_units>millimolar</PDBx:conc_units> <PDBx:sol_id>protein</PDBx:sol_id> </PDBx:pdbx_exptl_crystal_grow_comp> <PDBx:pdbx_exptl_crystal_grow_comp comp_id="3" crystal_id="4"> <PDBx:comp_name>NaCl</PDBx:comp_name> <PDBx:conc>0.2</PDBx:conc> <PDBx:conc_range xsi:nil="true" /> <PDBx:conc_units>molar</PDBx:conc_units> <PDBx:sol_id>protein</PDBx:sol_id> </PDBx:pdbx_exptl_crystal_grow_comp> <PDBx:pdbx_exptl_crystal_grow_comp comp_id="1" crystal_id="4"> <PDBx:comp_name>PEG 4000</PDBx:comp_name> <PDBx:conc>12.5</PDBx:conc> <PDBx:conc_range xsi:nil="true" /> <PDBx:conc_units>percent_weight_by_volume</PDBx:conc_units> <PDBx:sol_id>precipitant</PDBx:sol_id> </PDBx:pdbx_exptl_crystal_grow_comp> <PDBx:pdbx_exptl_crystal_grow_comp comp_id="2" crystal_id="4"> <PDBx:comp_name>MES</PDBx:comp_name> <PDBx:conc>0.1</PDBx:conc> <PDBx:conc_range xsi:nil="true" /> <PDBx:conc_units>molar</PDBx:conc_units> <PDBx:sol_id>precipitant</PDBx:sol_id> </PDBx:pdbx_exptl_crystal_grow_comp> </PDBx:pdbx_exptl_crystal_grow_compCategory> A common name for the component of the solution. protein in buffer acetic acid The concentration value of the solution component. 200. 0.1 The concentration range of the solution component. 200. - 230. 0.1 - 0.2 The concentration units for the solution component. millimolar percent_weight_by_volume milligrams_per_milliliter An identifier for the solution to which the given solution component belongs. The value of attribute comp_id in category exptl_crystal_grow_comp must uniquely identify each item in the PDBX_EXPTL_CRYSTAL_GROW_COMP list. Note that this item need not be a number; it can be any unique identifier. 1 2 This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. Data items in the PDBX_EXPTL_CRYSTAL_GROW_SOL category record details about the solutions that were 'mixed' to produce the crystal. Example 1 <PDBx:pdbx_exptl_crystal_grow_solCategory> <PDBx:pdbx_exptl_crystal_grow_sol crystal_id="1" sol_id="protein"> <PDBx:pH>7.5</PDBx:pH> <PDBx:volume>0.5</PDBx:volume> <PDBx:volume_units>microliter</PDBx:volume_units> </PDBx:pdbx_exptl_crystal_grow_sol> <PDBx:pdbx_exptl_crystal_grow_sol crystal_id="1" sol_id="precipitant"> <PDBx:pH>7.3</PDBx:pH> <PDBx:volume>0.5</PDBx:volume> <PDBx:volume_units>microliter</PDBx:volume_units> </PDBx:pdbx_exptl_crystal_grow_sol> <PDBx:pdbx_exptl_crystal_grow_sol crystal_id="1" sol_id="reservoir"> <PDBx:pH>7.3</PDBx:pH> <PDBx:volume>0.5</PDBx:volume> <PDBx:volume_units>milliliter</PDBx:volume_units> </PDBx:pdbx_exptl_crystal_grow_sol> </PDBx:pdbx_exptl_crystal_grow_solCategory> The pH of the solution. 7.2 The volume of the solution. 200. 0.1 The volume units of the solution. milliliter micoliter This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. An identifier for this solution (e.g. precipitant, reservoir, macromolecule) Data items in the pdbx_exptl_pd record information about powder sample preparations. A description of preparation steps for producing the diffraction specimen from the sample. Include any procedures related to grinding, sieving, spray drying, etc. POLYCRYSTAL SLURRY wet grinding in acetone sieved through a 44 micron (325 mesh/inch) sieve spray dried in water with 1% clay The pH at which the powder sample was prepared. The range of pH values at which the sample was prepared. Used when a point estimate of pH is not appropriate. 5.6 - 6.4 The value of attribute entry_id in category pdbx_exptl_pd uniquely identifies a record in the PDBX_EXPTL_PD category. Data items in the PDBX_FAMILY_GROUP_INDEX category record the family membership in family groups. Example 1 - <PDBx:pdbx_family_group_indexCategory> <PDBx:pdbx_family_group_index family_prd_id="FAM_0000001" id="FGR_0000001"></PDBx:pdbx_family_group_index> <PDBx:pdbx_family_group_index family_prd_id="FAM_0000002" id="FGR_0000001"></PDBx:pdbx_family_group_index> <PDBx:pdbx_family_group_index family_prd_id="FAM_0000021" id="FGR_0000001"></PDBx:pdbx_family_group_index> <PDBx:pdbx_family_group_index family_prd_id="FAM_0000022" id="FGR_0000002"></PDBx:pdbx_family_group_index> <PDBx:pdbx_family_group_index family_prd_id="FAM_0000023" id="FGR_0000002"></PDBx:pdbx_family_group_index> </PDBx:pdbx_family_group_indexCategory> This data item is a reference to the BIRD identifier for families. This data item is a pointer to attribute family_prd_id in category pdbx_reference_molecule_family in the pdbx_reference_molecule category. This data item is the identifier for the a group of related BIRD families. Data items in the PDBX_FAMILY_PRD_AUDIT category records the status and tracking information for this family. Example 1 - <PDBx:pdbx_family_prd_auditCategory> <PDBx:pdbx_family_prd_audit action_type="Create family" date="2011-12-01" family_prd_id="FAM_0000001"> <PDBx:annotator>JY</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_family_prd_audit> <PDBx:pdbx_family_prd_audit action_type="Modify sequence" date="2011-12-05" family_prd_id="FAM_0000001"> <PDBx:annotator>MZ</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_family_prd_audit> </PDBx:pdbx_family_prd_auditCategory> The initials of the annotator creating of modifying the family. JO SJ KB Additional details decribing this change. Revise molecule sequence. An identifier for the wwPDB site creating or modifying the family. RCSB PDBE PDBJ BMRB PDBC The action associated with this audit record. The date associated with this audit record. This data item is a pointer to attribute family_prd_id in category pdbx_reference_molecule_family in the pdbx_reference_molecule category. Data items in the PDBX_FEATURE_ASSEMBLY category records information about properties pertaining to this structural assembly. Example 1 - Biological process for functional assembly <PDBx:pdbx_feature_assemblyCategory> <PDBx:pdbx_feature_assembly id="1"> <PDBx:assembly_id>b1</PDBx:assembly_id> <PDBx:feature>nitrogen metabolism</PDBx:feature> <PDBx:feature_assigned_by>GO</PDBx:feature_assigned_by> <PDBx:feature_citation_id>GO</PDBx:feature_citation_id> <PDBx:feature_name>biological process</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_assembly> </PDBx:pdbx_feature_assemblyCategory> The value of attribute assembly_id in category pdbx_feature_assembly references an assembly definition in category STRUCT_BIOL The value of attribute feature_name in category pdbx_feature_assembly. attribute feature_assigned_by in category pdbx_feature_assembly identifies the individual, organization or program that assigned the feature. attribute feature_citation_id in category pdbx_feature_assembly is a reference to a citation in the CITATION category attribute feature_identifier in category pdbx_feature_assembly_range is an additional identifier used to identify or accession this feature. attribute feature_name in category pdbx_feature_assembly identifies a feature by name. attribute feature_software_id in category pdbx_feature_assembly is a reference to an application described in the SOFTWARE category. attribute feature_type in category pdbx_feature_assembly identifies the type of feature. The value of attribute id in category pdbx_feature_assembly uniquely identifies a feature in the PDBX_FEATURE_ASSEMBLY category. Data items in the PDBX_FEATURE_DOMAIN category records information about properties pertaining to this structure domain. Example 1 - SCOP data for PDB Entry 1KIP domain d1kipa_ <PDBx:pdbx_feature_domainCategory> <PDBx:pdbx_feature_domain id="1"> <PDBx:domain_id>d1kipa_</PDBx:domain_id> <PDBx:feature>All beta proteins</PDBx:feature> <PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by> <PDBx:feature_citation_id>scop</PDBx:feature_citation_id> <PDBx:feature_name>class</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_domain> <PDBx:pdbx_feature_domain id="2"> <PDBx:domain_id>d1kipa_</PDBx:domain_id> <PDBx:feature>Immunoglobulin-like beta-sandwich</PDBx:feature> <PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by> <PDBx:feature_citation_id>scop</PDBx:feature_citation_id> <PDBx:feature_name>fold</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_domain> <PDBx:pdbx_feature_domain id="3"> <PDBx:domain_id>d1kipa_</PDBx:domain_id> <PDBx:feature>Immunoglobulin</PDBx:feature> <PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by> <PDBx:feature_citation_id>scop</PDBx:feature_citation_id> <PDBx:feature_name>superfamily</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_domain> <PDBx:pdbx_feature_domain id="4"> <PDBx:domain_id>d1kipa_</PDBx:domain_id> <PDBx:feature>V set domains (antibody variable domain-like)</PDBx:feature> <PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by> <PDBx:feature_citation_id>scop</PDBx:feature_citation_id> <PDBx:feature_name>family</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_domain> <PDBx:pdbx_feature_domain id="5"> <PDBx:domain_id>d1kipa_</PDBx:domain_id> <PDBx:feature>Immunoglobulin light chain kappa variable domain</PDBx:feature> <PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by> <PDBx:feature_citation_id>scop</PDBx:feature_citation_id> <PDBx:feature_name>domain</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_domain> <PDBx:pdbx_feature_domain id="6"> <PDBx:domain_id>d1kipa_</PDBx:domain_id> <PDBx:feature>Mouse (Mus musculus), cluster 4</PDBx:feature> <PDBx:feature_assigned_by>SCOP</PDBx:feature_assigned_by> <PDBx:feature_citation_id>scop</PDBx:feature_citation_id> <PDBx:feature_name>species</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_domain> </PDBx:pdbx_feature_domainCategory> The value of attribute id in category pdbx_feature_domain references a domain definition in category PDBX_DOMAIN. The value of attribute feature_name in category pdbx_feature_domain. attribute feature_assigned_by in category pdbx_feature_domain identifies the individual, organization or program that assigned the feature. attribute feature_citation_id in category pdbx_feature_domain is a reference to a citation in the CITATION category. attribute feature_identifier in category pdbx_feature_domain is an additional identifier used to identify or accession this feature. attribute feature_name in category pdbx_feature_domain identifies a feature by name. attribute feature_software_id in category pdbx_feature_domain is a reference to an application described in the SOFTWARE category. attribute feature_type in category pdbx_feature_domain identifies the type of feature. The value of attribute id in category pdbx_feature_domain uniquely identifies a feature in the PDBX_FEATURE_DOMAIN category. Data items in the PDBX_FEATURE_ENTRY category records information about properties pertaining to this structure entry. Example 1 - Gene Ontology data by entry <PDBx:pdbx_feature_entryCategory> <PDBx:pdbx_feature_entry id="1"> <PDBx:feature>DNA binding activity</PDBx:feature> <PDBx:feature_assigned_by>GO</PDBx:feature_assigned_by> <PDBx:feature_citation_id>GO</PDBx:feature_citation_id> <PDBx:feature_name>molecular function</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_entry> <PDBx:pdbx_feature_entry id="2"> <PDBx:feature>regulation of transcription, DNA-dependent</PDBx:feature> <PDBx:feature_assigned_by>GO</PDBx:feature_assigned_by> <PDBx:feature_citation_id>GO</PDBx:feature_citation_id> <PDBx:feature_name>biological process</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> </PDBx:pdbx_feature_entry> </PDBx:pdbx_feature_entryCategory> The value of attribute feature_name in category pdbx_feature_entry. attribute feature_assigned_by in category pdbx_feature_entry identifies the individual, organization or program that assigned the feature. attribute feature_citation_id in category pdbx_feature_entry is a reference to a citation in the CITATION category attribute feature_identifier in category pdbx_feature_entry is an additional identifier used to identify or accession this feature. attribute feature_name in category pdbx_feature_entry identifies a feature by name. attribute feature_software_id in category pdbx_feature_entry is a reference to an application described in the SOFTWARE category. attribute feature_type in category pdbx_feature_entry identifies the type of feature. The value of attribute id in category pdbx_feature_entry uniquely identifies a feature in the PDBX_FEATURE_ENTRY category. Data items in the PDBX_FEATURE_MONOMER category records information about properties pertaining to particular monomers in this structure. Example 1 - <PDBx:pdbx_feature_monomerCategory> <PDBx:pdbx_feature_monomer id="1"> <PDBx:feature>129.4</PDBx:feature> <PDBx:feature_assigned_by>POPS</PDBx:feature_assigned_by> <PDBx:feature_citation_id>pops</PDBx:feature_citation_id> <PDBx:feature_name>SASA</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>ASP</PDBx:label_comp_id> <PDBx:label_seq_id>1</PDBx:label_seq_id> </PDBx:pdbx_feature_monomer> <PDBx:pdbx_feature_monomer id="1"> <PDBx:feature>35.5</PDBx:feature> <PDBx:feature_assigned_by>POPS</PDBx:feature_assigned_by> <PDBx:feature_citation_id>pops</PDBx:feature_citation_id> <PDBx:feature_name>SASA</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>2</PDBx:label_seq_id> </PDBx:pdbx_feature_monomer> <PDBx:pdbx_feature_monomer id="1"> <PDBx:feature>87.2</PDBx:feature> <PDBx:feature_assigned_by>POPS</PDBx:feature_assigned_by> <PDBx:feature_citation_id>pops</PDBx:feature_citation_id> <PDBx:feature_name>SASA</PDBx:feature_name> <PDBx:feature_type>value</PDBx:feature_type> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>3</PDBx:label_seq_id> </PDBx:pdbx_feature_monomer> </PDBx:pdbx_feature_monomerCategory> A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of attribute feature_name in category pdbx_feature_monomer. attribute feature_assigned_by in category pdbx_feature_monomer identifies the individual, organization or program that assigned the feature. attribute feature_citation_id in category pdbx_feature_monomer is a reference to a citation in the CITATION category. attribute feature_identifier in category pdbx_feature_monomer is an additional identifier used to identify or accession this feature. attribute feature_name in category pdbx_feature_monomer identifies a feature by name. attribute feature_software_id in category pdbx_feature_monomer is a reference to an application described in the SOFTWARE category. attribute feature_type in category pdbx_feature_monomer identifies the type of feature. A component of the identifier for the monomer. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for the monomer. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The value of attribute id in category pdbx_feature_monomer uniquely identifies a feature in the PDBX_FEATURE_MONOMER category. Data items in the PDBX_FEATURE_SEQUENCE_RANGE category records information about properties pertaining to this structure sequence_range. Example 1 - Secondary structure computed by program DSSP. <PDBx:pdbx_feature_sequence_rangeCategory> <PDBx:pdbx_feature_sequence_range id="1"> <PDBx:feature>4-helix (alpha-helix)</PDBx:feature> <PDBx:feature_assigned_by>DSSP</PDBx:feature_assigned_by> <PDBx:feature_name>secondary structure</PDBx:feature_name> <PDBx:feature_software_id>DSSP</PDBx:feature_software_id> <PDBx:feature_type>value</PDBx:feature_type> <PDBx:seq_range_id>H1</PDBx:seq_range_id> </PDBx:pdbx_feature_sequence_range> <PDBx:pdbx_feature_sequence_range id="2"> <PDBx:feature>hydrogen-bonded turn in beta-ladder</PDBx:feature> <PDBx:feature_assigned_by>DSSP</PDBx:feature_assigned_by> <PDBx:feature_name>secondary structure</PDBx:feature_name> <PDBx:feature_software_id>DSSP</PDBx:feature_software_id> <PDBx:feature_type>value</PDBx:feature_type> <PDBx:seq_range_id>T1</PDBx:seq_range_id> </PDBx:pdbx_feature_sequence_range> </PDBx:pdbx_feature_sequence_rangeCategory> The value of attribute feature_name in category pdbx_feature_sequence_range. attribute feature_assigned_by in category pdbx_feature_sequence_range identifies the individual, organization or program that assigned the feature. attribute feature_citation_id in category pdbx_feature_sequence_range is a reference to a citation in the CITATION category attribute feature_identifier in category pdbx_feature_sequence_range is an additional identifier used to identify or accession this feature. attribute feature_name in category pdbx_feature_sequence_range identifies a feature by name. attribute feature_software_id in category pdbx_feature_sequence_range is a reference to an application descripted in the SOFTWARE category. attribute feature_type in category pdbx_feature_sequence_range identifies the type of feature. The value of attribute seq_range_id in category pdbx_feature_sequence_range references a sequence_range definition in category PDBX_SEQUENCE_RANGE. The value of attribute id in category pdbx_feature_sequence_range uniquely identifies a feature in the PDBX_FEATURE_SEQUENCE_RANGE category Data items in the PDBX_HELICAL_SYMMETRY category record details about the helical symmetry group associated with this entry. Example 1 - <PDBx:pdbx_helical_symmetryCategory> <PDBx:pdbx_helical_symmetry entry_id="1ABC"> <PDBx:circular_symmetry>1</PDBx:circular_symmetry> <PDBx:dyad_axis>no</PDBx:dyad_axis> <PDBx:n_subunits_divisor>1</PDBx:n_subunits_divisor> <PDBx:number_of_operations>35</PDBx:number_of_operations> <PDBx:rise_per_n_subunits>6.10</PDBx:rise_per_n_subunits> <PDBx:rotation_per_n_subunits>131.84</PDBx:rotation_per_n_subunits> </PDBx:pdbx_helical_symmetry> </PDBx:pdbx_helical_symmetryCategory> Rotational n-fold symmetry about the helical axis. Two-fold symmetry perpendicular to the helical axis. Number of subunits used in the calculation of rise and rotation. Number of operations. Angular rotation (degrees) in N subunits Angular rotation (degrees) in N subunits This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PDBX_HELICAL_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_HELICAL_SYMMETRY. Example 1 - <PDBx:pdbx_helical_symmetry_depositor_infoCategory> <PDBx:pdbx_helical_symmetry_depositor_info entry_id="1ABC"> <PDBx:circular_symmetry>1</PDBx:circular_symmetry> <PDBx:dyad_axis>no</PDBx:dyad_axis> <PDBx:n_subunits_divisor>1</PDBx:n_subunits_divisor> <PDBx:number_of_operations>35</PDBx:number_of_operations> <PDBx:rise_per_n_subunits>6.10</PDBx:rise_per_n_subunits> <PDBx:rotation_per_n_subunits>131.84</PDBx:rotation_per_n_subunits> </PDBx:pdbx_helical_symmetry_depositor_info> </PDBx:pdbx_helical_symmetry_depositor_infoCategory> Rotational n-fold symmetry about the helical axis. Two-fold symmetry perpendicular to the helical axis. Number of subunits used in the calculation of rise and rotation. Number of operations. Angular rotation (degrees) in N subunits Angular rotation (degrees) in N subunits A flag to indicate that this data is relevant to the current entry This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PDBX_HYBRID category are used to describe the chimeric characteristics of a DNA/RNA structure. Example 1 - based on NDB entry AHJ068 <PDBx:pdbx_hybridCategory> <PDBx:pdbx_hybrid id="1"> <PDBx:residue_names>G01 C02</PDBx:residue_names> <PDBx:strand_id>A</PDBx:strand_id> <PDBx:sugar_name>R</PDBx:sugar_name> </PDBx:pdbx_hybrid> <PDBx:pdbx_hybrid id="2"> <PDBx:residue_names>G01 C02</PDBx:residue_names> <PDBx:strand_id>B</PDBx:strand_id> <PDBx:sugar_name>R</PDBx:sugar_name> </PDBx:pdbx_hybrid> <PDBx:pdbx_hybrid id="3"> <PDBx:residue_names>G03 T04 A05 T06 A07 C08 G09 C10</PDBx:residue_names> <PDBx:strand_id>A</PDBx:strand_id> <PDBx:sugar_name>D</PDBx:sugar_name> </PDBx:pdbx_hybrid> <PDBx:pdbx_hybrid id="4"> <PDBx:residue_names>G03 T04 A05 T06 A07 C08 G09 C10</PDBx:residue_names> <PDBx:strand_id>B</PDBx:strand_id> <PDBx:sugar_name>D</PDBx:sugar_name> </PDBx:pdbx_hybrid> </PDBx:pdbx_hybridCategory> List of residues + number (see example) which have the same sugar group in a particular strand. C01 C02 C03 Strand id. A Name of sugar group of residue. deoxyribonuclease D ribonuclease R arabinose ARA ID code. 1 Data items in the PDBX_INHIBITOR_INFO category are still used until the 'entity' categories are entered into the database, even though the inhibitor is repeated. Example 1 - based on NDB entry ... <PDBx:pdbx_inhibitor_infoCategory> <PDBx:pdbx_inhibitor_info id="1"> <PDBx:name>N-ACETYL-DEOXYTHYMIDINE</PDBx:name> <PDBx:num_per_asym_unit>1</PDBx:num_per_asym_unit> </PDBx:pdbx_inhibitor_info> </PDBx:pdbx_inhibitor_infoCategory> Name of inhibitor. N-ACETYL-DEOXYTHYMIDINE ADP Number of inhibitor molecules per asymmetric unit. 1 Serial number. 1 Data items in the PDBX_ION_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated. Example 1 - based on NDB entry DDH048 <PDBx:pdbx_ion_infoCategory> <PDBx:pdbx_ion_info id="1"> <PDBx:name>MG</PDBx:name> <PDBx:numb_per_asym_unit>3</PDBx:numb_per_asym_unit> </PDBx:pdbx_ion_info> </PDBx:pdbx_ion_infoCategory> Name of ion. MG Number of ion molecules per asymmetric unit. 1 2 3 Serial number. 1 Data items in the PDBX_LINKED_ENTITY category record information about molecules composed of linked entities. Example: 1 Actinomycin <PDBx:pdbx_linked_entityCategory> <PDBx:pdbx_linked_entity linked_entity_id="L1"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:name>Actinomycin D</PDBx:name> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_linked_entity> </PDBx:pdbx_linked_entityCategory> Broadly defines the function of this molecule. Description of this molecule. A name of the molecule. thiostrepton The identifier used by the PDB corresponding to the chemical definition for the molecule. PRD_000001 Defines the structural classification of this molecule. peptide-like macrolide The value of attribute linked_entity_id in category pdbx_linked_entity is the unique identifier for the molecule represented as a collection of linked entities. Data items in the PDBX_LINKED_ENTITY_INSTANCE_LIST category identify instance molecules represented as linked entities within an entry. Example 1 - <PDBx:pdbx_linked_entity_instance_listCategory> <PDBx:pdbx_linked_entity_instance_list asym_id="X" instance_id="1" linked_entity_id="L1"></PDBx:pdbx_linked_entity_instance_list> <PDBx:pdbx_linked_entity_instance_list asym_id="Y" instance_id="1" linked_entity_id="L1"></PDBx:pdbx_linked_entity_instance_list> <PDBx:pdbx_linked_entity_instance_list asym_id="Z" instance_id="1" linked_entity_id="L1"></PDBx:pdbx_linked_entity_instance_list> </PDBx:pdbx_linked_entity_instance_listCategory> A reference to attribute id in category struct_asym in the STRUCT_ASYM category. A B The value of attribute instance_id in category pdbx_linked_entity_instance_list is identifies a particular molecule instance within an entry. The value of attribute linked_entity_id in category pdbx_linked_entity_instance_list is a reference to the identifier for a molecule represented as a linked entity. Data items in the PDBX_LINKED_ENTITY_LINK_LIST category give details about the linkages with molecules represented as linked entities. Example 1 - quinoxaline <PDBx:pdbx_linked_entity_link_listCategory> <PDBx:pdbx_linked_entity_link_list link_id="1" linked_entity_id="L1"> <PDBx:atom_id_1>N</PDBx:atom_id_1> <PDBx:atom_id_2>C</PDBx:atom_id_2> <PDBx:comp_id_1>DSN</PDBx:comp_id_1> <PDBx:comp_id_2>QUI</PDBx:comp_id_2> <PDBx:component_1>1</PDBx:component_1> <PDBx:component_2>2</PDBx:component_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>2</PDBx:entity_id_2> <PDBx:entity_seq_num_1>1</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2 xsi:nil="true" /> <PDBx:link_class>PN</PDBx:link_class> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_linked_entity_link_list> <PDBx:pdbx_linked_entity_link_list link_id="2" linked_entity_id="L1"> <PDBx:atom_id_1>N</PDBx:atom_id_1> <PDBx:atom_id_2>C</PDBx:atom_id_2> <PDBx:comp_id_1>DSN</PDBx:comp_id_1> <PDBx:comp_id_2>QUI</PDBx:comp_id_2> <PDBx:component_1>1</PDBx:component_1> <PDBx:component_2>3</PDBx:component_2> <PDBx:entity_id_1>1</PDBx:entity_id_1> <PDBx:entity_id_2>3</PDBx:entity_id_2> <PDBx:entity_seq_num_1>5</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2 xsi:nil="true" /> <PDBx:link_class>PN</PDBx:link_class> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_linked_entity_link_list> </PDBx:pdbx_linked_entity_link_listCategory> The atom identifier/name in the first of the two entities containing the linkage. The atom identifier/name in the second of the two entities containing the linkage. The component identifier in the first of the two entities containing the linkage. For polymer entities, this data item is a pointer to attribute mon_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. For non-polymer entities, this data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The component identifier in the second of the two entities containing the linkage. For polymer entities, this data item is a pointer to attribute mon_id in category entity_poly_seq in the ENTITY_POLY_SEQ category. For non-polymer entities, this data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The entity component identifier for the first of two entities containing the linkage. The entity component identifier for the second of two entities containing the linkage. A description of special aspects of a linkage between these entities in this molecule. The entity id of the first of the two entities joined by the linkage. This data item is a pointer to attribute entity_id in category pdbx_linked_entity_list in the PDBX_LINKED_ENTITY_LIST category. The entity id of the second of the two entities joined by the linkage. This data item is a pointer to attribute entity_id in category pdbx_linked_entity_list in the PDBX_LINKED_ENTITY_LIST category. For a polymer entity, the sequence number in the first of the two entities containing the linkage. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. For a polymer entity, the sequence number in the second of the two entities containing the linkage. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. A code indicating the entity types involved in the linkage. The bond order target for the chemical linkage. The value of attribute link_id in category pdbx_linked_entity_link_list uniquely identifies linkages between entities with a molecule. The value of attribute linked_entity_id in category pdbx_linked_entity_link_list is a reference attribute linked_entity_id in category pdbx_linked_entity_list in the PDBX_LINKED_ENTITY_LIST category. Data items in the PDBX_LINKED_ENTITY_LIST category record the list of entity constituents for this molecule. Example: 1 <PDBx:pdbx_linked_entity_listCategory> <PDBx:pdbx_linked_entity_list component_id="1" entity_id="1" linked_entity_id="L1"></PDBx:pdbx_linked_entity_list> <PDBx:pdbx_linked_entity_list component_id="2" entity_id="2" linked_entity_id="L1"></PDBx:pdbx_linked_entity_list> <PDBx:pdbx_linked_entity_list component_id="3" entity_id="3" linked_entity_id="L1"></PDBx:pdbx_linked_entity_list> </PDBx:pdbx_linked_entity_listCategory> Additional details about this entity within this molecule. The component number of this entity within the molecule. The value of attribute ref_entity_id in category pdbx_linked_entity_list is a unique identifier the a constituent entity within this reference molecule. The value of attribute linked_entity_id in category pdbx_linked_entity_list is a reference attribute linked_entity_id in category pdbx_linked_entity in the PDBX_LINKED_ENTITY category. Data items in the PDBX_MISSING_ATOM_NONPOLY category list the atoms missing in nonpolymer residues. This is a completely derived category. Do not edit. Identifier of missing atom. Identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. The model number for the given residue The value of attribute id in category pdbx_missing_atom_nonpoly must uniquely identify each item in the PDBX_MISSING_ATOM_NONPOLY list. This is an integer serial number. Data items in the PDBX_MISSING_ATOM_POLY category lists atoms missing in polymer residues. This is a completely derived category. Do not edit. Identifier of missing atom. Identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number for the given residue The value of attribute id in category pdbx_missing_atom_poly must uniquely identify each item in the PDBX_MISSING_ATOM_POLY list. This is an integer serial number. Provides a place-holder for PDB REMARK 465 data. An index in the sequence specified in category ENTITY_POLY_SEQ. PDB chain ID. PDB model ID. PDB chain ID. PDB chain ID. PDB chain ID. Data items in the PDBX_MOLECULE category identify reference molecules within a PDB entry. Example 1 - <PDBx:pdbx_moleculeCategory> <PDBx:pdbx_molecule asym_id="X" instance_id="1" prd_id="PRD_050001"></PDBx:pdbx_molecule> <PDBx:pdbx_molecule asym_id="Y" instance_id="1" prd_id="PRD_050001"></PDBx:pdbx_molecule> <PDBx:pdbx_molecule asym_id="Z" instance_id="1" prd_id="PRD_050001"></PDBx:pdbx_molecule> </PDBx:pdbx_moleculeCategory> A reference to attribute linked_entity_id in category pdbx_linked_entity in the PDBX_LINKED_ENTITY category. 1 2 A reference to attribute id in category struct_asym in the STRUCT_ASYM category. A B The value of attribute instance_id in category pdbx_molecule is identifies a particular molecule in the molecule list. The value of attribute prd_id in category pdbx_molecule is the PDB accession code for this reference molecule. Data items in the PDBX_MOLECULE_FEATURES category record features of molecules within a PDB entry. Example 1 - <PDBx:pdbx_molecule_featuresCategory> <PDBx:pdbx_molecule_features prd_id="PRD_000001"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:name>Actinomycin D</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_molecule_features> </PDBx:pdbx_molecule_featuresCategory> Broadly defines the function of the molecule. Additional details describing the molecule. A name of the molecule. thiostrepton Defines the structural classification of the molecule. Peptide-like Macrolide The value of attribute prd_id in category pdbx_molecule_features is the accession code for this reference molecule. Data items in the PDBX_MOLECULE_FEATURES_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_MOLECULE_FEATURES. Example 1 - <PDBx:pdbx_molecule_features_depositor_infoCategory> <PDBx:pdbx_molecule_features_depositor_info entity_id="1"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:name>Actinomycin D</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_molecule_features_depositor_info> </PDBx:pdbx_molecule_features_depositor_infoCategory> Broadly defines the function of the molecule. Additional details describing the molecule. A name of the molecule. thiostrepton Defines the structural classification of the molecule. peptide-like macrolide The value of attribute entity_id in category pdbx_molecule_features_depositor_info is a reference to to the entity identifier for this molecule. Data items in the PDBX_NA_STRAND_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated. Example 1 - based on NDB entry DDH048 <PDBx:pdbx_na_strand_infoCategory> <PDBx:pdbx_na_strand_info id="1"> <PDBx:fract_NA_strand_per_asym_unit>half</PDBx:fract_NA_strand_per_asym_unit> <PDBx:num_of_NA_strands_per_asym_unit>2</PDBx:num_of_NA_strands_per_asym_unit> <PDBx:num_of_NA_strands_per_biol_unit>2</PDBx:num_of_NA_strands_per_biol_unit> </PDBx:pdbx_na_strand_info> </PDBx:pdbx_na_strand_infoCategory> Size of drug molecules per asymmetric unit. half whole quarter Number of na strands per asymmetric unit. Number of na strands per biological unit. Serial number. Data items in the PDBX_NA_STRUCT_KEYWDS category record give details about structural features of the NA. Example 1 - based on NDB entry UDJ031 <PDBx:pdbx_na_struct_keywdsCategory> <PDBx:pdbx_na_struct_keywds entry_id="UDJ031"> <PDBx:conformation_type>B</PDBx:conformation_type> <PDBx:special_feature> FLIPPED-OUT BASES, INTERMOLECULAR BASE TRIPLET</PDBx:special_feature> <PDBx:strand_description>DOUBLE HELIX</PDBx:strand_description> </PDBx:pdbx_na_struct_keywds> </PDBx:pdbx_na_struct_keywdsCategory> Provides overall idea about conformation type of NA. Also, it identifies tRNAs by assigning a 'T' here. A Describes special features of NA. LOOP LOOPS INTERNAL LOOP HAIRPIN LOOP BULGES FLIPPED-OUT BASES STICKY ENDS OVERHANGING BASES 5'-UU-OVERHANG CYCLIC PARALLEL HELIX CONTINUOUS HELIX HAMMERHEAD HAMMERHEAD DNA-RNA RIBOZYME RNA HAMMERHEAD RIBOZYME TETRAPLEX PARALLEL-STRANDED TETRAPLEX TETRAMERIC AGGREGATE BASE TRIPLET INTERMOLECULAR BASE TRIPLET NICKED SHIFTED BASE PAIRS OPEN HELIX OPEN CLOSED BASE INTERCALATED RACEMATE A-DNA LIKE CONFORMATION AT TERMINI Z-DNA STEM 2'-5' PHOSPHODIESTER BOND Gives general structural description of NA. DOUBLE HELIX This data item is a pointer to attribute id in category entry in the ENTRY category. Items in the assigned_chem_shift_list category provide information about a list of reported assigned chemical shift values. The value assigned as the error for all 13C chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.1 The value assigned as the error for all 15N chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.2 The value assigned as the error for all 19F chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.01 The value assigned as the error for all 1H chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.01 The value assigned as the error for all 2H chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.01 The value assigned as the error for all 31P chemical shifts reported in the chemical shift list. The value reported for this tag will be inserted during annotation into the assigned chemical shift error column in the table of assigned chemical shifts. 0.1 Pointer to '_pdbx_nmr_chem_shift_reference.id' Pointer to '_pdbx_nmr_exptl_sample_conditions.conditions_id' Pointer to 'pdbx_nmr_exptl_sample_conditions.label'. sample conditions one The name of the file submitted with a deposition that contains the quantitative chemical shift data. Text describing the reported assigned chemical shifts. Method used to derive the estimated error in the reported chemical shifts. A descriptive label that uniquely identifies a list of reported assigned chemical shifts. assigned chem shift set 1 Pointer to '_entry.ID' 2DSX An integer value that uniquely identifies a list of assigned chemical shifts from other sets of assigned chemical shifts in the entry. Items in the chem_shift_experiment category provide pointers to the NMR experiments and samples used to collect the data for a set of reported assigned chemical shifts. The name of an experiment used to determine the data reported. Physical state of the sample either anisotropic or isotropic. Pointer to '_pdbx_nmr_exptl_sample.solution_id' Pointer to '_pdbx_nmr_assigned_chem_shift_list.ID' Pointer to '_entry.id' 2DSX Pointer to '_pdbx_nmr_exptl.experiment.id' Items in the pdbx_nmr_chem_shift_ref category provide the chemical shift referencing values used in assigning the chemical shift positions for peaks in spectral peak lists and assigned atom chemical shifts. Example 1 <PDBx:pdbx_nmr_chem_shift_refCategory> <PDBx:pdbx_nmr_chem_shift_ref atom_isotope_number="1" atom_type="H" chem_shift_reference_id="1" entry_id="1ABC" mol_common_name="DSS"> <PDBx:atom_group>methyl protons</PDBx:atom_group> <PDBx:chem_shift_units>ppm</PDBx:chem_shift_units> <PDBx:chem_shift_val>0.000</PDBx:chem_shift_val> <PDBx:indirect_shift_ratio>1.00000000</PDBx:indirect_shift_ratio> <PDBx:ref_method>external</PDBx:ref_method> <PDBx:ref_type>direct</PDBx:ref_type> </PDBx:pdbx_nmr_chem_shift_ref> <PDBx:pdbx_nmr_chem_shift_ref atom_isotope_number="13" atom_type="C" chem_shift_reference_id="1" entry_id="1ABC" mol_common_name="DSS"> <PDBx:atom_group>methyl protons</PDBx:atom_group> <PDBx:chem_shift_units>ppm</PDBx:chem_shift_units> <PDBx:chem_shift_val>0.000</PDBx:chem_shift_val> <PDBx:indirect_shift_ratio>0.251449530</PDBx:indirect_shift_ratio> <PDBx:ref_method>external</PDBx:ref_method> <PDBx:ref_type>indirect</PDBx:ref_type> </PDBx:pdbx_nmr_chem_shift_ref> <PDBx:pdbx_nmr_chem_shift_ref atom_isotope_number="15" atom_type="N" chem_shift_reference_id="1" entry_id="1ABC" mol_common_name="DSS"> <PDBx:atom_group>methyl protons</PDBx:atom_group> <PDBx:chem_shift_units>ppm</PDBx:chem_shift_units> <PDBx:chem_shift_val>0.000</PDBx:chem_shift_val> <PDBx:indirect_shift_ratio>0.101329118</PDBx:indirect_shift_ratio> <PDBx:ref_method>external</PDBx:ref_method> <PDBx:ref_type>indirect</PDBx:ref_type> </PDBx:pdbx_nmr_chem_shift_ref> </PDBx:pdbx_nmr_chem_shift_refCategory> Group of atoms within a molecule whose chemical shift was used as the standard chemical shift reference for the defined observed nuclei. methyl protons Units for the chemical shift value assigned to the atoms of the chemical shift reference. ppm Value assigned to the chemical shift of the reference compound. 4.78 An uniform correction value that was applied because of an extenuating circumstance such as data collection at an unusual temperature. 0.1 The axis of the external chemical shift reference sample relative to the static field (Bo) of the spectrometer. parallel External chemical shift references are defined as either located within the sample (e.g., as a capillary) or external to the sample and are inserted into the spectrometer before, after, or both before and after the sample containing the molecular system studied in the entry. insert at center of experimental sample tube The geometrical shape of the external reference sample. spherical The Chi value used in calculating the chemical shift referencing values for nuclei that are referenced indirectly. The values used should be those recommended by the IUPAC Taskforce on the deposition of data to the public databases (Markley, et al. Pure and Appl. Chem. 70, 117-142 (1998). 0.25144953 The rank of the chemical shift reference. A primary reference is the one used in reporting the data. A secondary reference would be the compound in the sample or used as an external reference. 1 If a correction value is applied to calculate the reported chemical shifts the source of the correction (pH; temperature; etc.). temperature The chemical shift reference may be either internal (the compound is located in the sample) or external (the compound is in a container external to the sample). internal The reference type may be either direct (against a value measured with a chemical compound) or indirect (calculated from chemical shift ratios). direct Solvent used for the external reference sample. CHCL3 The mass number for the chemical element defined by the tag '_pdbx_nmr_chem_shift_ref.atom_type' or any of its related tags. 2 The value for this tag is a standard IUPAC abbreviation for an element (i.e., H, C, P, etc). H Pointer to '_pdbx_nmr_chem_shift_reference.id' Pointer to '_entry.id' 2DSX Common name or abbreviation used in the literature for the molecule used as a chemical shift reference. DSS Items in the chem_shift_reference category define a set of chemical shift referencing parameters. Example 1 <PDBx:pdbx_nmr_chem_shift_referenceCategory> <PDBx:pdbx_nmr_chem_shift_reference entry_id="1ABC" id="1"> <PDBx:details>External DSS sample</PDBx:details> <PDBx:label>chemical_shift_reference_</PDBx:label> </PDBx:pdbx_nmr_chem_shift_reference> </PDBx:pdbx_nmr_chem_shift_referenceCategory> A value indicating if 13C chemical shifts are being deposited and if IUPAC chemical shift referencing was used. This item is a user interface item that is used to trigger the automated population of chemical shift referencing tags if IUPAC chemical shift referencing parameters have been used. yes with IUPAC referencing Text providing additional information regarding the reported chemical shift referencing values or methods. A descriptive label that uniquely identifies this list of chemical shift referencing parameters used in reporting assigned chemical shifts and other chemical shift data. chemical_shift_reference_1 A value indicating if 15N chemical shifts are being deposited and if IUPAC chemical shift referencing was used. This item is a user interface item that is used to trigger the automated population of chemical shift referencing tags if IUPAC chemical shift referencing parameters have been used. yes A value indicating if chemical shifts other than 1H, 13C, 15N, or 31P are being deposited. A value indicating if 31P chemical shifts are being deposited and if IUPAC chemical shift referencing was used. This item is a user interface item that is used to trigger the automated population of chemical shift referencing tags if IUPAC chemical shift referencing parameters have been used. A value indicating if 1H chemical shifts are being deposited and if IUPAC chemical shift referencing was used. This item is a user interface item that is used to trigger the automated population of chemical shift referencing tags if IUPAC chemical shift referencing parameters have been used. Please indicate yes or no$ if you are depositing 1H chemical shifts. Pointer to '_entry.id' 2SNS An integer value that uniquely identifies a set of chemical shift reference values from other sets of chemical shift referencing values. Items in the chem_shift_software category provide pointers to the software category and methods category. Name given to the software. The name should match the name provided when the software was described in the software category. Pointer to '_pdbx_nmr_assigned_chem_shift_list.id' 1 Pointer to '_entry.id' 2DSX Pointer to '_pdbx_nmr_software.ordinal' 1 The table in this section is used to describe the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include both the name of the software and the version used. This example describes the software used in the MCP-1 study. <PDBx:pdbx_nmr_computingCategory> <PDBx:pdbx_nmr_computing entry_id="1ABC"> <PDBx:collection>UXNMR</PDBx:collection> <PDBx:collection_version>940501.3</PDBx:collection_version> <PDBx:processing>FELIX</PDBx:processing> <PDBx:processing_version>1.1</PDBx:processing_version> </PDBx:pdbx_nmr_computing> </PDBx:pdbx_nmr_computingCategory> Enter the name of the software used for data collection. UXNMR XWINNMR Enter the version of the software used for data collection. 940501.3 2.1 Enter the name of the software used for data analysis. AURELIA NMRPip? NMRCap? ANSIG Enter the version of the software used for data analysis. 3.3 Enter the name of the software used for iterative relaxation matrix methods. IRMA CORMA MARDIGRAS Enter the version of the software used for iterative relaxation matrix methods. 2.2 Enter the name of the software used for data processing. XWINNMR FELIX95 FELIX98 NMRPipe AZARA Enter the version of the software used for data processing. 2.1 Enter the name of the software used for refinement. DISCOVER GROMOS CHARMM Enter the version of the software used for refinement. 3.1 Enter the name of the software used to calculate the structure. X-PLOR DIANA DSPACE DISGEO Enter the version of the software used to calculate the structure. 3.1 The entry ID for the structure determination. Items in the pdbx_nmr_constraint_file category record the name of the constraint file, the software used to calculate conformers with the constraint file, and the characteristics of the constraints in the constraint file. Number of constraints of this type and subtype in the file. 2045 Local unique identifier for the listed constraint file. Name of the software application that the listed constraint file is used as input. XPLOR-NIH Pointer to attribute ordinal in category software Name of the uploaded file that contains the constraint data. sns_constraints.txt Specific type of constraint. NOE The general type of constraint (distance, torsion angle, RDC, etc.) distance Pointer to '_entry.id' 2SNS This section provides a tabulation of constraint data. This example uses the data from the MCP-1 structure determination. Remember this is a dimer so there are intersubunit constraints as well as intrasubunit constraints. <PDBx:pdbx_nmr_constraintsCategory> <PDBx:pdbx_nmr_constraints entry_id="1ABC"> <PDBx:NOE_constraints_total>4458</PDBx:NOE_constraints_total> <PDBx:NOE_intraresidue_total_count>1144</PDBx:NOE_intraresidue_total_count> <PDBx:NOE_long_range_total_count>1356</PDBx:NOE_long_range_total_count> <PDBx:NOE_medium_range_total_count>1004</PDBx:NOE_medium_range_total_count> <PDBx:NOE_sequential_total_count>272</PDBx:NOE_sequential_total_count> <PDBx:protein_phi_angle_constraints_total_count>96</PDBx:protein_phi_angle_constraints_total_count> </PDBx:pdbx_nmr_constraints> </PDBx:pdbx_nmr_constraintsCategory> The total number of nucleic acid alpha-angle constraints used in the final structure calculation. 18 The total number of nucleic acid beta-angle constraints used in the final structure calculation. 24 The total number of nucleic acid chi-angle constraints used in the final structure calculation. 15 The total number of nucleic acid delta-angle constraints used in the final structure calculation. 15 The total number of nucleic acid epsilon-angle constraints used in the final structure calculation. 31 The total number of nucleic acid gamma-angle constraints used in the final structure calculation. 12 The total number of nucleic acid other-angle constraints used in the final structure calculation. 5 The total number of nucleic acid sugar pucker constraints used in the final structure calculation. 10 The total number of all NOE constraints used in the final structure calculation. 4458 The total number of interentity, NOE constraints used in the final structure calculation. This field should only be if system is complex -i.e more than one entity e.g. a dimer or ligand-protein complex 272 Describe the method used to quantify the NOE and ROE values. NOE buildup curves with 50, 75, 150 ms mixing times were analyzed. Noesy cross peak intensities were classified into three different catagories with distances of 1.8-2.7 A, 1.8-3.5 A, 1.8- 5.0 A for strong, medium and weak NOEs. The total number of all intraresidue, [i-j]=0, NOE constraints used in the final structure calculation. 1144 The total number of long range [i-j]>5 NOE constraints used in the final structure calculation. 1356 The total number of medium range 1<[i-j]<=5 NOE constraints used in the final structure calculation. 682 Describe any corrections that were made to the NOE data for motional averaging. Replace with item example text Describe any corrections made for pseudoatoms Pseudo-atoms nomenclature and corrections according to Wuethrich, Billeter, and Braun, J. Mol.Biol.(1983) 169, 949-961. Pseudoatoms were not used. The total number of sequential, [i-j]=1, NOE constraints used in the final structure calculation. 1004 The total number of disulfide bond constraints used in the final structure calculation. 3 The total number of hydrogen bond constraints used in the final structure calculation. 6 The total number of chi angle constraints used in the final structure calculation. 66 The total number of other angle constraints used in the final structure calculation. 0 The total number of phi angle constraints used in the final structure calculation 96 The total number of psi angle constraints used in the final structure calculation. 0 You can leave this blank as an ID will be assigned by the MSD to the constraint file. Experimental details of the NMR study that have not been described elsewhere in this deposition. Additional details describing the NMR experiment. This structure was determined using standard 2D homonuclear techniques. The structure was determined using triple-resonance NMR spectroscopy. The entry ID for the structure determination. This category contains the information that describes the ensemble of deposited structures. If only an average structure has been deposited skip this section. This example uses the data from the MCP-1 study. <PDBx:pdbx_nmr_ensembleCategory> <PDBx:pdbx_nmr_ensemble entry_id="1ABC"> <PDBx:conformer_selection_criteria>structures with the least restraint violations</PDBx:conformer_selection_criteria> <PDBx:conformers_calculated_total_number>40</PDBx:conformers_calculated_total_number> <PDBx:conformers_submitted_total_number>20</PDBx:conformers_submitted_total_number> <PDBx:representative_conformer>1</PDBx:representative_conformer> </PDBx:pdbx_nmr_ensemble> </PDBx:pdbx_nmr_ensembleCategory> The average number of constraint violations on a per residue basis for the ensemble. 0.25 The average number of constraints per residue for the ensemble 30.2 The average distance restraint violation for the ensemble. 0.11 The average torsion angle constraint violation for the ensemble. 2.4 By highlighting the appropriate choice(s), describe how the submitted conformer (models) were selected. structures with the lowest energy structures with the least restraint violations structures with acceptable covalent geometry structures with favorable non-bond energy target function back calculated data agree with experimental NOESY spectrum all calculated structures submitted The submitted conformer models are the 25 structures with the lowest energy. The submitted conformer models are those with the fewest number of constraint violations. The total number of conformer (models) that were calculated in the final round. 40 The number of conformer (models) that are submitted for the ensemble. 20 Describe the method used to calculate the distance constraint violation statistics, i.e. are they calculated over all the distance constraints or calculated for violations only? Statistics were calculated over all of the distance constraints. Statistics were calculated for violations only The maximum distance constraint violation for the ensemble. 0.4 The maximum lower distance constraint violation for the ensemble. 0.3 The maximum torsion angle constraint violation for the ensemble. 4 The maximum upper distance constraint violation for the ensemble. 0.4 The number of the conformer identified as most representative. 20 This item describes the method used to calculate the torsion angle constraint violation statistics. i.e. are the entered values based on all torsion angle or calculated for violations only? Statistics were calculated over all the torsion angle constraints. Statistics were calculated for torsion angle constraints violations only. Leave this blank as the ID is provided by the MSD Structural statistics are derived from molecular dynamics and simulated annealing programs. This example is derived from the MCP-1 structure calculation statistics. For this structure the statistics were calculated over residues 5-69 for both the monomer and dimer . <PDBx:pdbx_nmr_ensemble_rmsCategory> <PDBx:pdbx_nmr_ensemble_rms entry_id="1ABC"> <PDBx:atom_type>all heavy atoms</PDBx:atom_type> <PDBx:chain_range_begin>A</PDBx:chain_range_begin> <PDBx:chain_range_end>A</PDBx:chain_range_end> <PDBx:distance_rms_dev>0.22</PDBx:distance_rms_dev> <PDBx:distance_rms_dev_error>0.06</PDBx:distance_rms_dev_error> <PDBx:residue_range_begin>5</PDBx:residue_range_begin> <PDBx:residue_range_end>69</PDBx:residue_range_end> </PDBx:pdbx_nmr_ensemble_rms> </PDBx:pdbx_nmr_ensemble_rmsCategory> Statistics are often calculated over only some of the atoms, e.g. backbone, or heavy atoms. Describe which type of atoms are used for the statistical analysis. backbone atoms heavy atoms The bond angle rmsd to the target values for the ensemble. 0.60 The error in the bond angle rmsd. 0.01 The beginning chain id. A The ending chain id: A Describe the method for calculating the coordinate average rmsd. Replace with item example text The covalent bond rmsd to the target value for the ensemble. 0.0066 The error in the covalent bond rmsd. 0.0001 The dihedral angle rmsd to the target values for the ensemble. 0.66 The error of the rmsd dihedral angles. 0.07 The distance rmsd to the mean structure for the ensemble of structures. 0.22 The error in the distance rmsd. 0.07 The improper torsion angle rmsd to the target values for the ensemble. 0.64 The error in the improper torsion angle rmsd. 0.04 The peptide planarity rmsd. 0.11 The error in the peptide planarity rmsd. 0.05 Structure statistics are often calculated only over the well-ordered region(s) of the biopolymer. Portions of the macromolecule are often mobile and disordered, hence they are excluded in calculating the statistics. To define the range(s) over which the statistics are calculated, enter the beginning residue number(s): e.g. if the regions used were 5-32 and 41-69, enter 5,41 5 41 The ending residue number: e.g. 32,69. 32 69 '?' In this section, enter information on those experiments that were used to generate constraint data. For each NMR experiment indicate which sample and which sample conditions were used for the experiment. This example was taken from the MCP-1 study. <PDBx:pdbx_nmr_exptlCategory> <PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="1" solution_id="3"> <PDBx:type>3D_15N-separated_NOESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="2" solution_id="1"> <PDBx:type>3D_13C-separated_NOESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl conditions_id="2" experiment_id="3" solution_id="1"> <PDBx:type>4D_13C/15N-separated_NOESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="4" solution_id="1"> <PDBx:type>4D_13C-separated_NOESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="5" solution_id="1"> <PDBx:type>3D_15N-separated_ROESY</PDBx:type> </PDBx:pdbx_nmr_exptl> <PDBx:pdbx_nmr_exptl conditions_id="1" experiment_id="6" solution_id="3"> <PDBx:type>3D_13C-separated_ROESY</PDBx:type> </PDBx:pdbx_nmr_exptl> </PDBx:pdbx_nmr_exptlCategory> Physical state of the sample either anisotropic or isotropic. isotropic Pointer to '_pdbx_nmr_spectrometer.spectrometer_id' The type of NMR experiment. 2D NOESY 3D_15N-separated_NOESY 3D_13C-separated_NOESY 4D_13C-separated_NOESY 4D_13C/15N-separated_NOESY 3D_15N-separated_ROESY 3D_13C-separated_ROESY HNCA-J HNHA DQF-COSY P-COSY PE-COSY E-COSY The number to identify the set of sample conditions. 1 2 3 A numerical ID for each experiment. 1 2 3 The solution_id from the Experimental Sample to identify the sample that these conditions refer to. [Remember to save the entries here before returning to the Experimental Sample form] 1 2 3 The chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name. Example 1 This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. <PDBx:pdbx_nmr_exptl_sampleCategory> <PDBx:pdbx_nmr_exptl_sample component="MCP-1" solution_id="1"> <PDBx:concentration>2</PDBx:concentration> <PDBx:concentration_units>mM</PDBx:concentration_units> <PDBx:isotopic_labeling>U-15N,13C</PDBx:isotopic_labeling> </PDBx:pdbx_nmr_exptl_sample> <PDBx:pdbx_nmr_exptl_sample component="H2O" solution_id="1"> <PDBx:concentration>90</PDBx:concentration> <PDBx:concentration_units>&#37;</PDBx:concentration_units> <PDBx:isotopic_labeling xsi:nil="true" /> </PDBx:pdbx_nmr_exptl_sample> <PDBx:pdbx_nmr_exptl_sample component="D2O" solution_id="1"> <PDBx:concentration>10</PDBx:concentration> <PDBx:concentration_units>&#37;</PDBx:concentration_units> <PDBx:isotopic_labeling xsi:nil="true" /> </PDBx:pdbx_nmr_exptl_sample> </PDBx:pdbx_nmr_exptl_sampleCategory> Example 2 This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. <PDBx:pdbx_nmr_exptl_sampleCategory> <PDBx:pdbx_nmr_exptl_sample component="MCP-1" solution_id="2"> <PDBx:concentration>1</PDBx:concentration> <PDBx:concentration_units>mM</PDBx:concentration_units> <PDBx:isotopic_labeling>U-50&#37; 15N</PDBx:isotopic_labeling> </PDBx:pdbx_nmr_exptl_sample> <PDBx:pdbx_nmr_exptl_sample component="H2O" solution_id="2"> <PDBx:concentration>90</PDBx:concentration> <PDBx:concentration_units>&#37;</PDBx:concentration_units> <PDBx:isotopic_labeling xsi:nil="true" /> </PDBx:pdbx_nmr_exptl_sample> <PDBx:pdbx_nmr_exptl_sample component="D2O" solution_id="2"> <PDBx:concentration>10</PDBx:concentration> <PDBx:concentration_units>&#37;</PDBx:concentration_units> <PDBx:isotopic_labeling xsi:nil="true" /> </PDBx:pdbx_nmr_exptl_sample> </PDBx:pdbx_nmr_exptl_sampleCategory> The concentration value of the component. 2.0 2.7 0.01 Estimate for the standard error associated with the concentration value of the sample component. 0.2 The concentration range for the component. 2.0-2.2 2.7-3.5 0.01-0.05 The concentration units of the component. mg/mL for mg per milliliter mM for millimolar % for percent by volume The isotopic composition of each component, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labled biomolecule is designated by NA: U-13C; NA-K,H U-13C,15N U-2H The name of each component in the sample ribonuclease DNA strand 1 TRIS buffer sodium chloride H2O D2O The name (number) of the sample. 1 2 3 The experimental conditions used to for each sample. Each set of conditions is identified by a numerical code. This example was taken from a pH stability study. <PDBx:pdbx_nmr_exptl_sample_conditionsCategory> <PDBx:pdbx_nmr_exptl_sample_conditions conditions_id="1"> <PDBx:ionic_strength>25mM NaCl</PDBx:ionic_strength> <PDBx:pH>7</PDBx:pH> <PDBx:pressure>ambient</PDBx:pressure> <PDBx:temperature>298</PDBx:temperature> </PDBx:pdbx_nmr_exptl_sample_conditions> <PDBx:pdbx_nmr_exptl_sample_conditions conditions_id="2"> <PDBx:ionic_strength>25mM NaCl</PDBx:ionic_strength> <PDBx:pH>3</PDBx:pH> <PDBx:pressure>ambient</PDBx:pressure> <PDBx:temperature>298</PDBx:temperature> </PDBx:pdbx_nmr_exptl_sample_conditions> </PDBx:pdbx_nmr_exptl_sample_conditionsCategory> General details describing conditions of both the sample and the environment during measurements. The high salinity of the sample may have contributed to overheating of the sample during experiments with long saturation periods like the TOCSY experiments. The ionic strength at which the NMR data were collected -in lieu of this enter the concentration and identity of the salt in the sample. Estimate of the standard error for the value for the sample ionic strength. 0.2 Units for the value of the sample condition ionic strength.. M A descriptive label that uniquely identifies this set of sample conditions. conditions_1 The pH at which the NMR data were collected. 3.1 7.0 Estimate of the standard error for the value for the sample pH. 0.05 Units for the value of the sample condition pH. pH The pressure at which NMR data were collected. ambient 1atm Estimate of the standard error for the value for the sample pressure. 0.01 The units of pressure at which NMR data were collected. Pa atm Torr The temperature (in Kelvin) at which NMR data were collected. 298 Estimate of the standard error for the value for the sample temperature. 0.2 Units for the value of the sample condition temperature. K The condition number as defined above. 1 2 3 The final force constants, including units, employed for the various experimental constraints, covalent geometry constraints, and the non-bonded interaction terms in the target function used for simulated annealing. This example is taken from a study of BAF, a dimeric DNA binding protein. The final force constants in the target function used for simulated annealing are: Experimental Constraint terms: Distance (NOE,H-bonds), Torsion angles, J coupling, 13C shifts, 1H shifts, Dipolar coupling, D isotope shifts Covalent Geometry Constraint terms: Bond lengths, Angles, Impropers Non-bonded Interaction terms: van der Waals, Type of van der Waals term, Conformational database potential, Radius of gyration. <PDBx:pdbx_nmr_force_constantsCategory> <PDBx:pdbx_nmr_force_constants entry_id="1ABC"> <PDBx:covalent_geom_bond_term>1000.</PDBx:covalent_geom_bond_term> <PDBx:covalent_geom_bond_term_units>kcal/mol/A**2</PDBx:covalent_geom_bond_term_units> <PDBx:exptl_13C_shift_term>0.5</PDBx:exptl_13C_shift_term> <PDBx:exptl_13C_shift_term_units>kcal/mol/ppm**2</PDBx:exptl_13C_shift_term_units> <PDBx:exptl_1H_shift_term>7.5</PDBx:exptl_1H_shift_term> <PDBx:exptl_1H_shift_term_units>kcal/mol/ppm**2</PDBx:exptl_1H_shift_term_units> <PDBx:exptl_J_coupling_term>1.</PDBx:exptl_J_coupling_term> <PDBx:exptl_J_coupling_term_units>kcal/mol/Hz**2</PDBx:exptl_J_coupling_term_units> <PDBx:exptl_distance_term>30.</PDBx:exptl_distance_term> <PDBx:exptl_distance_term_units>kcal/mol/A**2</PDBx:exptl_distance_term_units> <PDBx:exptl_torsion_angles_term>200.</PDBx:exptl_torsion_angles_term> <PDBx:exptl_torsion_angles_term_units>kcal/mol/rad**2</PDBx:exptl_torsion_angles_term_units> <PDBx:non-bonded_inter_van_der_Waals_term_type>4.</PDBx:non-bonded_inter_van_der_Waals_term_type> <PDBx:non-bonded_inter_van_der_Waals_term_units>kcal/mol/A**4</PDBx:non-bonded_inter_van_der_Waals_term_units> </PDBx:pdbx_nmr_force_constants> </PDBx:pdbx_nmr_force_constantsCategory> The final force constant for covalent geometry angle constraints term employed in the target function used for simulated annealing. 500 The units for the force constant for the covalent geometry angle constraints term. kcal/mol/rad**2 The final force constant for the covalent geometry bond length constraints term employed in the target function used for simulated annealing. 1000 The units for the force constant for the covalent geometry bond length constraints term. kcal/mol/A**2 The final force constant for covalent geometry impropers contstraints term employed in the target function used for simulated annealing. 500 The units for the force constant for the covalent geometry impropers constraints term. kcal/mol/rad**2 The final force constant for 13C shift constraints term employed in the target function used for simulated annealing. 0.5 The units for the force constant for the 13C shift constraints term. kcal/mol/ppm**2 The final force constant for 1H shift constraints term employed in the target function used for simulated annealing. 7.5 The units for the force constant for the 1H shift constraints term. kcal/mol/ppm**2 The final force constant for Deuterium isotope shift constraints term employed in the target function used for simulated annealing. 0.5 The units for the force constant for the Deuterium isotope shift constraints term. kcal/mol/ppb**2 The final force constant for J coupling term employed in the target function used for simulated annealing. 1 The units for the force constant for the J coupling term. kcal/mol/Hz**2 The final force constant for dipolar coupling constraint term employed in the target function used for simulated annealing. 1 The units for the force constant for the dipolar coupling constraints term. kcal/mol/Hz**2 The final force constant for distance (NOEs) constraints term employed in the target function used for simulated annealing. 30 The units for the force constant for the distance constraints term. kcal/mol/ A**2 The final force constant for the torsion angle term employed in the target function used for simulated annealing. 200 The units for the force constant for the torsion angle constraints term. kcal/mol/rad**2 The force constant used for the non-bonded interaction conformational database potential term employed in the target function used for simulated annealing. 1.0 The force constant used for the non-bonded interaction radius of gyration term employed in the target function used for simulated annealing. 100 The units for the force constant for the radius of gyration term. kcal/mol/ A**2 The force constant used for the non-bonded interaction van der Waals term employed in the target function used for simulated annealing. 4 The type of van der Waals term employed in the target function used for simulated annealing. quartic The units for the force constant for the van der Waals term. kcal/mol/ A**4 You can leave this blank as an ID will be assigned by the RCSB. Describe the method and details of the refinement of the deposited structure. This example is drawn from the MCP-1 structure. <PDBx:pdbx_nmr_refineCategory> <PDBx:pdbx_nmr_refine entry_id="1ABC" software_ordinal="1"> <PDBx:method>torsion angle dynamics</PDBx:method> </PDBx:pdbx_nmr_refine> </PDBx:pdbx_nmr_refineCategory> Additional details about the NMR refinement. Additional comments about the NMR refinement can be placed here, e.g. the structures are based on a total of 3344 restraints, 3167 are NOE-derived distance constraints, 68 dihedral angle restraints,109 distance restraints from hydrogen bonds. The method used to determine the structure. distance geometry simulated annealing molecular dynamics matrix relaxation torsion angle dynamics You can leave this blank as an ID will be assigned by the RCSB to the constraint file. Pointer to attribute ordinal in category software An average structure is often calculated in addition to the ensemble, or one of the ensemble is selected as a representative structure. This section describes selection of the representative structure. This example is drawn from the MCP-1 structure. <PDBx:pdbx_nmr_representativeCategory> <PDBx:pdbx_nmr_representative entry_id="1ABC"> <PDBx:conformer_id>15</PDBx:conformer_id> <PDBx:selection_criteria>lowest energy</PDBx:selection_criteria> </PDBx:pdbx_nmr_representative> </PDBx:pdbx_nmr_representativeCategory> If a member of the ensemble has been selected as a representative structure, identify it by its model number. 15 By highlighting the appropriate choice(s), describe the criteria used to select this structure as a representative structure, or if an average structure has been calculated describe how this was done. The structure closest to the average. The structure with the lowest energy was selected. The structure with the fewest number of violations was selected. A minimized average structure was calculated. msd will assign the ID. Complete description of each NMR sample, including the solvent system used. This example was taken from the study of MCP-1 which is a dimer under the conditions studied. Three solutions with different isotope compositions were studied. <PDBx:pdbx_nmr_sample_detailsCategory> <PDBx:pdbx_nmr_sample_details solution_id="1"> <PDBx:contents>2 mM U-15N,13C, H2O 90 &#37;, D2O 10 &#37;</PDBx:contents> <PDBx:solvent_system>MCP-1</PDBx:solvent_system> </PDBx:pdbx_nmr_sample_details> <PDBx:pdbx_nmr_sample_details solution_id="2"> <PDBx:contents>1 mM U-50&#37; 15N, MCP-1 1 mM U-50&#37; 13C, H2O 90 &#37;, D2O 10 &#37;</PDBx:contents> <PDBx:solvent_system>MCP-1</PDBx:solvent_system> </PDBx:pdbx_nmr_sample_details> <PDBx:pdbx_nmr_sample_details solution_id="3"> <PDBx:contents>2 mM U-15N, H2O 90 &#37;, D2O 10 &#37;</PDBx:contents> <PDBx:solvent_system>MCP-1</PDBx:solvent_system> </PDBx:pdbx_nmr_sample_details> </PDBx:pdbx_nmr_sample_detailsCategory> A complete description of each NMR sample. Include the concentration and concentration units for each component (include buffers, etc.). For each component describe the isotopic composition, including the % labeling level, if known. For example: 1. Uniform (random) labeling with 15N: U-15N 2. Uniform (random) labeling with 13C, 15N at known labeling levels: U-95% 13C;U-98% 15N 3. Residue selective labeling: U-95% 15N-Thymine 4. Site specific labeling: 95% 13C-Ala18, 5. Natural abundance labeling in an otherwise uniformly labeled biomolecule is designated by NA: U-13C; NA-K,H 2mM Ribonuclease U-15N,13C; 50mM phosphate buffer NA; 90% H2O, 10% D2O Brief description of the sample providing additional information not captured by other items in the category. The added glycerol was used to raise the viscosity of the solution to 1.05 poisson. A value that uniquely identifies this sample from the other samples listed in the entry. 15N_sample The solvent system used for this sample. 90% H2O, 10% D2O A descriptive term for the sample that defines the general physical properties of the sample. bicelle The name (number) of the sample. 1 2 3 Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used. This example describes the software used in the MCP-1 study. <PDBx:pdbx_nmr_softwareCategory> <PDBx:pdbx_nmr_software ordinal="1"> <PDBx:authors>Bruker</PDBx:authors> <PDBx:classification>collection</PDBx:classification> <PDBx:name>UXNMR</PDBx:name> <PDBx:version>940501.3</PDBx:version> </PDBx:pdbx_nmr_software> <PDBx:pdbx_nmr_software ordinal="2"> <PDBx:authors>Hare</PDBx:authors> <PDBx:classification>processing</PDBx:classification> <PDBx:name>FELIX</PDBx:name> <PDBx:version>1.1</PDBx:version> </PDBx:pdbx_nmr_software> <PDBx:pdbx_nmr_software ordinal="3"> <PDBx:authors>Kraulis</PDBx:authors> <PDBx:classification>data analysis</PDBx:classification> <PDBx:name>ANSIG</PDBx:name> <PDBx:version>3.0</PDBx:version> </PDBx:pdbx_nmr_software> <PDBx:pdbx_nmr_software ordinal="4"> <PDBx:authors>Brunger</PDBx:authors> <PDBx:classification>structure calculation</PDBx:classification> <PDBx:name>X-PLOR</PDBx:name> <PDBx:version>3.8</PDBx:version> </PDBx:pdbx_nmr_software> </PDBx:pdbx_nmr_softwareCategory> The name of the authors of the software used in this procedure. Brunger Guentert The purpose of the software. collection processing data analysis structure solution refinement iterative matrix relaxation Text description of the software. The name of the software used for the task. ANSIG AURELIA AZARA CHARMM CoMAND CORMA DIANA DYANA DSPACE DISGEO DGII DISMAN DINOSAUR DISCOVER FELIX FT_NMR GROMOS IRMA MARDIGRAS NMRPipe SA UXNMR VNMR X-PLOR XWINNMR The version of the software. 940501.3 2.1 An ordinal index for this category 1 2 Items in the pdbx_nmr_software_task category provide information about software workflow in the NMR experiment. Pointer to '_entry.id' 2SNS Pointer to attribute ordinal in category software 1 A word or brief phrase that describes the task that a software application was used to carry out. chemical shift assignment Items in the spectral_dim category describe the parameters of each dimension in the NMR experiment used to generate the spectral peak list. The mass number for the specified atom. 13 The center frequency offset for the spectral dimension specified. 4.76 Pointer to '_pdbx_nmr_spectral_dim.id'. The spectral dimension in a reduced dimensionality experiment that is the source of the magnetization that has been encoded. 3 Code describing how information from one spectral dimension has been encoded in another dimension in for example a reduced dimensionality experiment. CO in CA The magnetization linkage ID is used to designate dimensions of a multidimensional NMR experiment where the nuclei observed in the dimensions are directly linked by a one bond scalar coupling. For example, the amide proton and amide nitrogen in an 1H-15N HSQC experiment. 1 The width of the spectral window observed in Hz. 6132.234 The units for the sweep width value (Hz or ppm) Hz ppm The type of spectral folding/aliasing that was used or occurred when the spectrum was collected. aliased folded not observed The value for this tag is a standard IUPAC abbreviation for an element (i.e., H, C, N, P, etc). C Pointer to '_entry.id' 2DSX An integer value that specifies the dimension of a multidimensional NMR spectrum. 2 Pointer to '_pdbx_nmr_spectral_peak_list.id' A code defining the type of nuclei that would be expected to be observed in the spectral region observed in the dimension of the spectrum. CA Items in the pdbx_nmr_spectral_peak_list category provide information about a list of reported spectral peak characteristic values. Pointer to '_pdbx_nmr_exptl_sample_conditions.conditions_id' Pointer to 'pdbx_nmr_exptl_sample_conditions.label'. sample conditions one The name of the file submitted with a deposition that contains the quantitative data for a spectral peak list. Text describing the reported list of spectral peaks. Pointer to '_pdbx_nmr_exptl.experiment_id' A descriptive label that uniquely identifies a list of reported spectral peaks. peak list 1 Number of dimension in the spectrum from which the peak list was extracted. 3 Pointer to '_pdbx_nmr_exptl_sample.solution_id' The data format used to represent the spectral peak data as ASCII text in the text block that is the value to the '_Spectral_peak_list.Text_data' tag. Pointer to '_entry.id' 2dsx Unique identifier for a spectral peak list in an entry. Items in the pdbx_nmr_spectral_peak_software category provide pointers to the software category and methods category where descriptions of software applications and methods can be found. Pointer to '_entry.id' 2DSX Pointer to '_pdbx_nmr_software.ordinal' Pointer to '_pdbx_nmr_spectral_peak_list.id' The details about each spectrometer used to collect data for this deposition. The instruments described here are the ones used for the MCP-1 studies. <PDBx:pdbx_nmr_spectrometerCategory> <PDBx:pdbx_nmr_spectrometer spectrometer_id="1"> <PDBx:field_strength>600</PDBx:field_strength> <PDBx:type>Bruker AMX</PDBx:type> </PDBx:pdbx_nmr_spectrometer> <PDBx:pdbx_nmr_spectrometer spectrometer_id="2"> <PDBx:field_strength>500</PDBx:field_strength> <PDBx:type>Bruker AMX</PDBx:type> </PDBx:pdbx_nmr_spectrometer> </PDBx:pdbx_nmr_spectrometerCategory> A text description of the NMR spectrometer. The field strength in MHz of the spectrometer 360 400 500 600 750 800 850 900 950 1000 The name of the manufacturer of the spectrometer. Varian Bruker JEOL GE The model of the NMR spectrometer. AVANCE AVANCE II AVANCE III AVANCE III HD WH WM AM AMX DMX DRX MSL OMEGA OMEGA PSG GX GSX A AL EC EX LA ECP VXRS UNITY UNITYPLUS INOVA A label that uniquely identifies the NMR spectrometer from other spectrometers listed in the entry. Select the instrument manufacturer(s) and the model(s) of the NMR(s) used for this work. Bruker WH Bruker WM Bruker AM Bruker AMX Bruker DMX Bruker DRX Bruker MSL Bruker AVANCE GE Omega GE Omega PSG JEOL GX JEOL GSX JEOL A JEOL AL JEOL EC JEOL EX JEOL LA JEOL ECP Varian VXRS Varian UNITY Varian UNITYplus Varian INOVA other Assign a numerical ID to each instrument. 1 2 3 Items in the pdbx_nmr_systematic_chem_shift_offset category define chemical shift offsets that systematically affect all chemical shifts in a set of assigned chemical shifts for a specific nuclei. Pointer to '_pdbx_nmr_assigned_chem_shift_list.id' 1 Mass number for the atom defined by the '.Atom_type' tag with a systematic chemical shift offset. 1 The kind of atom to which the chemical shift offset value applies. amide nitrogens Pointer to '_entry.id' 2DSX The kind of chemical shift offset that should be applied to all chemical shifts observed for a specific type of atom. TROSY effect Chemical shift value that has been applied to all of the reported chemical shifts to bring their values in line with values expected to be observed for the chemical shift referencing that was used. 0.75 Error in the reported chemical shift offset value used. 0.0067 An ordinal identifier uniquely identifying records in the pdbx_nmr_systematic_chem_shift_offset category. 1 Items in the pdbx_nmr_upload category provide information about the data files uploaded by a depositor using the deposition system. This item defines the kind of data in the file uploaded for deposition. The directory path and file name for the data file that is to be uploaded. t1_relaxation_1.txt The syntax or format of the file that is uploaded. NMR-STAR v3 Unique code assigned to the file being uploaded by the depositor and that contains data that will be incorporated into this entry. Pointer to '_entry.id' 2DSX The PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities. Example 1 - <PDBx:pdbx_nonpoly_schemeCategory> <PDBx:pdbx_nonpoly_scheme asym_id="C" ndb_seq_num="100"> <PDBx:auth_mon_id>HOH</PDBx:auth_mon_id> <PDBx:auth_seq_num>100</PDBx:auth_seq_num> <PDBx:entity_id>3</PDBx:entity_id> <PDBx:mon_id>HOH</PDBx:mon_id> <PDBx:pdb_ins_code xsi:nil="true" /> <PDBx:pdb_mon_id>HOH</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>100</PDBx:pdb_seq_num> <PDBx:pdb_strand_id>C</PDBx:pdb_strand_id> </PDBx:pdbx_nonpoly_scheme> </PDBx:pdbx_nonpoly_schemeCategory> Author provided residue identifier. This value may differ from the PDB residue identifier and may not correspond to residue identification within the coordinate records. Author provided residue numbering. This value may differ from the PDB residue number and may not correspond to residue numbering within the coordinate records. Pointer to attribute label_entity_id in category atom_site. Pointer to attribute label_comp_id in category atom_site. PDB insertion code. PDB residue identifier. PDB residue number. PDB strand/chain id. Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 NDB/RCSB residue number. The information in this category is exclusively used to store the HET records of a PDB file. This record will be generated by the PROGRAM. Example 1 - based on NDB entry DDLB57. <PDBx:pdbx_nonstandard_listCategory> <PDBx:pdbx_nonstandard_list id="BR" label_asym_id="A"> <PDBx:label_seq_num>3</PDBx:label_seq_num> <PDBx:number_atoms_nh>1</PDBx:number_atoms_nh> </PDBx:pdbx_nonstandard_list> <PDBx:pdbx_nonstandard_list id="BR" label_asym_id="C"> <PDBx:label_seq_num>27</PDBx:label_seq_num> <PDBx:number_atoms_nh>1</PDBx:number_atoms_nh> </PDBx:pdbx_nonstandard_list> <PDBx:pdbx_nonstandard_list id="CPT" label_asym_id="E"> <PDBx:label_seq_num>49</PDBx:label_seq_num> <PDBx:number_atoms_nh>3</PDBx:number_atoms_nh> </PDBx:pdbx_nonstandard_list> <PDBx:pdbx_nonstandard_list id="CPT" label_asym_id="F"> <PDBx:label_seq_num>50</PDBx:label_seq_num> <PDBx:number_atoms_nh>3</PDBx:number_atoms_nh> </PDBx:pdbx_nonstandard_list> </PDBx:pdbx_nonstandard_listCategory> Chain id of the nonstandard group used by the author. Residue number of the nonstandard group used by the author. Insertion code of het group. A Residue number of het group. 2 The number of non-hydrogen atoms in the het group. The value of attribute id in category pdbx_nonstandard_list must uniquely identify each item in the PDBX_NONSTANDARD_LIST list. For protein polymer entities, this is the three-letter code for amino acids. For nucleic acid polymer entities, this is the one-letter code for the bases. ala val A BR Chain ID of het group. A B Residue id of het group. 2 This is a place holder for the PDB COMPND. PDB COMPND record. BARNASE (G SPECIFIC ENDONUCLEASE) (E.C.3.1.27.-) MUTANT WITH SER 91 REPLACED BY ALA (S91A) NDB ID. 1 This is a place holder for the PDB SOURCE. PDB SOURCE record. EXPRESSED IN (ESCHERICHIA COLI) NDB ID. 1 Record details about each phasing set: (Note: the phasing set is different from data set. for example: if there are three data sets, the inflection point (IP), the peak (PK) and the high remote (HR), the combination of the phasing set will be IP_iso, PK_iso (the isomorphous repleacement with HR as 'native'), IP_ano, PK_ano and HR_ano (the anomalous difference with itself). Therefore, there are five set used for phasing. Example 1 - three wavelengths <PDBx:pdbx_phasing_MAD_setCategory> <PDBx:pdbx_phasing_MAD_set id="ISO_1"> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:reflns_acentric>5387</PDBx:reflns_acentric> <PDBx:reflns_centric>471</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ISO_2"> <PDBx:R_cullis_acentric>0.803</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.718</PDBx:R_cullis_centric> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:reflns_acentric>5365</PDBx:reflns_acentric> <PDBx:reflns_centric>469</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ISO_3"> <PDBx:R_cullis_acentric>0.658</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.500</PDBx:R_cullis_centric> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:reflns_acentric>5317</PDBx:reflns_acentric> <PDBx:reflns_centric>460</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ANO_1"> <PDBx:R_cullis_acentric>0.841</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:reflns_acentric>5278</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ANO_2"> <PDBx:R_cullis_acentric>0.649</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:reflns_acentric>5083</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set> <PDBx:pdbx_phasing_MAD_set id="ANO_3"> <PDBx:R_cullis_acentric>0.829</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:d_res_high>2.00</PDBx:d_res_high> <PDBx:d_res_low>22.60</PDBx:d_res_low> <PDBx:reflns_acentric>5329</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set> </PDBx:pdbx_phasing_MAD_setCategory> attribute R_cullis in category pdbx_phasing_MAD_set records R_cullis for MAD phasing. attribute R_cullis_acentric in category pdbx_phasing_MAD_set records R_cullis using acentric data for MAD phasing. attribute R_cullis_centric in category pdbx_phasing_MAD_set records R_cullis using centric data for MAD phasing. attribute R_kraut in category pdbx_phasing_MAD_set records R_kraut for MAD phasing. attribute r_kraut_acentric in category pdbx_phasing_MAD_set records r_kraut using acentric data for MAD phasing. attribute R_kraut_centric in category pdbx_phasing_MAD_set records r_kraut using centric data for MAD phasing. attribute d_res_high in category pdbx_phasing_MAD_set records the highest resolution for the phasing set. attribute d_res_low in category pdbx_phasing_MAD_set records the lowerest resolution for phasing set. attribute fom in category pdbx_phasing_MAD_set records the figure of merit for MAD phasing. attribute fom_acentric in category pdbx_phasing_MAD_set records the figure of merit using acentric data for MAD phasing. attribute fom_centric in category pdbx_phasing_MAD_set records the figure of merit using centric data for MAD phasing. attribute loc in category pdbx_phasing_MAD_set records lack of closure for MAD phasing. attribute loc_acentric in category pdbx_phasing_MAD_set records lack of closure using acentric data for MAD phasing. attribute loc_centric in category pdbx_phasing_MAD_set records lack of closure using centric data for MAD phasing. attribute number_of_sites in category pdbx_phasing_MAD_set records the number of site refined for the phasing set. attribute power in category pdbx_phasing_MAD_set records phasing power for MAD phasing. attribute power_acentric in category pdbx_phasing_MAD_set records phasing powe using acentric data for MAD phasing. attribute power_centric in category pdbx_phasing_MAD_set records phasing powe using centric data for MAD phasing. attribute reflns in category pdbx_phasing_MAD_set records the number of reflections used for MAD phasing. attribute reflns_acentric in category pdbx_phasing_MAD_set records the number of acentric reflections for MAD phasing. attribute reflns_centric in category pdbx_phasing_MAD_set records the number of centric reflections for MAD phasing. attribute id in category pdbx_phasing_MAD_set records phase set name for MAD phasing. The same as category pdbx_phasing_MAD_set, but broken into shells. Example 1 - three wavelengths (SHARP example) <PDBx:pdbx_phasing_MAD_set_shellCategory> <PDBx:pdbx_phasing_MAD_set_shell d_res_high="7.77" d_res_low="22.60" id="ISO_1"> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>0.000</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> <PDBx:reflns_acentric>64</PDBx:reflns_acentric> <PDBx:reflns_centric>23</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell d_res_high="5.67" d_res_low="7.77" id="ISO_1"> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>0.000</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> <PDBx:reflns_acentric>130</PDBx:reflns_acentric> <PDBx:reflns_centric>32</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell d_res_high="4.68" d_res_low="5.67" id="ISO_1"> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>0.000</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> <PDBx:reflns_acentric>182</PDBx:reflns_acentric> <PDBx:reflns_centric>27</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell d_res_high="4.07" d_res_low="4.68" id="ISO_1"> <PDBx:R_cullis_acentric>0.000</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>0.000</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> <PDBx:reflns_acentric>207</PDBx:reflns_acentric> <PDBx:reflns_centric>24</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell d_res_high="7.77" d_res_low="22.60" id="ANO_1"> <PDBx:R_cullis_acentric>0.610</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>1.804</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> <PDBx:reflns_acentric>62</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell d_res_high="5.67" d_res_low="7.77" id="ANO_1"> <PDBx:R_cullis_acentric>0.532</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>2.382</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> <PDBx:reflns_acentric>129</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell d_res_high="4.68" d_res_low="5.67" id="ANO_1"> <PDBx:R_cullis_acentric>0.673</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>1.858</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> <PDBx:reflns_acentric>178</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set_shell> <PDBx:pdbx_phasing_MAD_set_shell d_res_high="4.07" d_res_low="4.68" id="ANO_1"> <PDBx:R_cullis_acentric>0.755</PDBx:R_cullis_acentric> <PDBx:R_cullis_centric>0.000</PDBx:R_cullis_centric> <PDBx:power_acentric>1.605</PDBx:power_acentric> <PDBx:power_centric>0.000</PDBx:power_centric> <PDBx:reflns_acentric>204</PDBx:reflns_acentric> <PDBx:reflns_centric>0</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_set_shell> </PDBx:pdbx_phasing_MAD_set_shellCategory> attribute R_cullis in category pdbx_phasing_MAD_set_shell records R_cullis for MAD phasing. attribute R_cullis_acentric in category pdbx_phasing_MAD_set_shell records R_cullis using acentric data for MAD phasing. attribute R_cullis_centric in category pdbx_phasing_MAD_set_shell records R_cullis using centric data for MAD phasing. attribute R_kraut in category pdbx_phasing_MAD_set_shell records R_kraut for MAD phasing. attribute R_kraut_acentric in category pdbx_phasing_MAD_set_shell records R_kraut using acentric data for MAD phasing. attribute R_kraut_centric in category pdbx_phasing_MAD_set_shell records R_kraut using centric data for MAD phasing. attribute fom in category pdbx_phasing_MAD_set_shell records the figure of merit for MAD phasing. attribute fom_acentric in category pdbx_phasing_MAD_set_shell records the figure of merit using acentric data for MAD phasing. attribute fom_centric in category pdbx_phasing_MAD_set_shell records the figure of merit using centric data for MAD phasing. attribute loc in category pdbx_phasing_MAD_set_shell records lack of closure for MAD phasing. attribute loc_acentric in category pdbx_phasing_MAD_set_shell records lack of closure using acentric data for MAD phasing. attribute loc_centric in category pdbx_phasing_MAD_set_shell records lack of closure using centric data for MAD phasing. attribute power in category pdbx_phasing_MAD_set_shell records phasing power for MAD phasing. attribute power_acentric in category pdbx_phasing_MAD_set_shell records phasing power using acentric data for MAD phasing. attribute power_centric in category pdbx_phasing_MAD_set_shell records phasing power using centric data for MAD phasing. attribute reflns in category pdbx_phasing_MAD_set_shell records the number of reflections used for MAD phasing. attribute reflns_acentric in category pdbx_phasing_MAD_set_shell records the number of acentric reflections for MAD phasing. attribute reflns_centric in category pdbx_phasing_MAD_set_shell records the number of centric reflections for MAD phasing. attribute d_res_high in category pdbx_phasing_MAD_set_shell records the highest resolution for the phasing set. attribute d_res_low in category pdbx_phasing_MAD_set_shell records the lowerest resolution for phasing set. attribute id in category pdbx_phasing_MAD_set_shell records phase set name for MAD phasing. record the details (coordinates etc.) of anomalous scatters. Example 1 - anomalous scatters is Se <PDBx:pdbx_phasing_MAD_set_siteCategory> <PDBx:pdbx_phasing_MAD_set_site id="1"> <PDBx:Cartn_x>25.9407</PDBx:Cartn_x> <PDBx:Cartn_y>-0.103471</PDBx:Cartn_y> <PDBx:Cartn_z>17.4094</PDBx:Cartn_z> <PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol> <PDBx:b_iso>15.2561</PDBx:b_iso> <PDBx:occupancy>1</PDBx:occupancy> </PDBx:pdbx_phasing_MAD_set_site> <PDBx:pdbx_phasing_MAD_set_site id="2"> <PDBx:Cartn_x>30.6534</PDBx:Cartn_x> <PDBx:Cartn_y>6.62359</PDBx:Cartn_y> <PDBx:Cartn_z>9.93063</PDBx:Cartn_z> <PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol> <PDBx:b_iso>12.9102</PDBx:b_iso> <PDBx:occupancy>1</PDBx:occupancy> </PDBx:pdbx_phasing_MAD_set_site> <PDBx:pdbx_phasing_MAD_set_site id="3"> <PDBx:Cartn_x>-3.26506</PDBx:Cartn_x> <PDBx:Cartn_y>15.5546</PDBx:Cartn_y> <PDBx:Cartn_z>53.9529</PDBx:Cartn_z> <PDBx:atom_type_symbol>SE</PDBx:atom_type_symbol> <PDBx:b_iso>30.5239</PDBx:b_iso> <PDBx:occupancy>1</PDBx:occupancy> </PDBx:pdbx_phasing_MAD_set_site> </PDBx:pdbx_phasing_MAD_set_siteCategory> attribute Cartn_x in category pdbx_phasing_MAD_set_site records the X Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_x_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation X Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_y in category pdbx_phasing_MAD_set_site records the Y Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_y_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Y Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_z in category pdbx_phasing_MAD_set_site records the Z Cartesian coordinate of site obtained from MAD phasing. attribute Cartn_z_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Z Cartesian coordinate of site obtained from MAD phasing. attribute atom_type_symbol in category pdbx_phasing_MAD_set_site records the name of site obtained from MAD phasing. attribute b_iso in category pdbx_phasing_MAD_set_site records isotropic temperature factor parameterthe for the site obtained from MAD phasing. attribute b_iso_esd in category pdbx_phasing_MAD_set_site records estimated standard deviation of isotropic temperature factor parameterthe for the site obtained from MAD phasing. attribute fract_x in category pdbx_phasing_MAD_set_site records the X fractional coordinate of site obtained from MAD phasing. attribute fract_x_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation X fractional coordinate of site obtained from MAD phasing. attribute fract_y in category pdbx_phasing_MAD_set_site records the Y fractional coordinate of site obtained from MAD phasing. attribute fract_y_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Y fractional coordinate of site obtained from MAD phasing. attribute fract_z in category pdbx_phasing_MAD_set_site records the Z fractional coordinate of site obtained from MAD phasing. attribute fract_z_esd in category pdbx_phasing_MAD_set_site records the estimated standard deviation Z fractional coordinate of site obtained from MAD phasing. attribute occupancy in category pdbx_phasing_MAD_set_site records the fraction of the atom type presented at this site. attribute occupancy_esd in category pdbx_phasing_MAD_set_site records estimated standard deviation of the fraction of the atom type presented at this site. The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given atom site. record the phasing set. attribute id in category pdbx_phasing_MAD_set_site records the number of site obtained from MAD phasing. Data items in the PDBX_PHASING_MAD_SHELL category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved (note: the values are overall, but broken down into shells of resolution) Example 1 - <PDBx:pdbx_phasing_MAD_shellCategory> <PDBx:pdbx_phasing_MAD_shell d_res_high="7.77" d_res_low="22.60"> <PDBx:fom_acentric>0.886</PDBx:fom_acentric> <PDBx:fom_centric>0.641</PDBx:fom_centric> <PDBx:reflns_acentric>64</PDBx:reflns_acentric> <PDBx:reflns_centric>23</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_high="5.67" d_res_low="7.77"> <PDBx:fom_acentric>0.863</PDBx:fom_acentric> <PDBx:fom_centric>0.642</PDBx:fom_centric> <PDBx:reflns_acentric>132</PDBx:reflns_acentric> <PDBx:reflns_centric>32</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_high="4.68" d_res_low="5.67"> <PDBx:fom_acentric>0.842</PDBx:fom_acentric> <PDBx:fom_centric>0.737</PDBx:fom_centric> <PDBx:reflns_acentric>182</PDBx:reflns_acentric> <PDBx:reflns_centric>27</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_high="4.07" d_res_low="4.68"> <PDBx:fom_acentric>0.789</PDBx:fom_acentric> <PDBx:fom_centric>0.682</PDBx:fom_centric> <PDBx:reflns_acentric>209</PDBx:reflns_acentric> <PDBx:reflns_centric>24</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_high="3.65" d_res_low="4.07"> <PDBx:fom_acentric>0.772</PDBx:fom_acentric> <PDBx:fom_centric>0.633</PDBx:fom_centric> <PDBx:reflns_acentric>246</PDBx:reflns_acentric> <PDBx:reflns_centric>27</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_shell> <PDBx:pdbx_phasing_MAD_shell d_res_high="3.34" d_res_low="3.65"> <PDBx:fom_acentric>0.752</PDBx:fom_acentric> <PDBx:fom_centric>0.700</PDBx:fom_centric> <PDBx:reflns_acentric>260</PDBx:reflns_acentric> <PDBx:reflns_centric>31</PDBx:reflns_centric> </PDBx:pdbx_phasing_MAD_shell> </PDBx:pdbx_phasing_MAD_shellCategory> attribute R_cullis in category pdbx_phasing_MAD_shell records R_cullis for MAD phasing. attribute R_cullis_acentric in category pdbx_phasing_MAD_shell records R_cullis using acentric data for MAD phasing. attribute R_cullis_centric in category pdbx_phasing_MAD_shell records R_cullis using centric data for MAD phasing. attribute R_kraut in category pdbx_phasing_MAD_shell records R_kraut for MAD phasing. attribute r_kraut_acentric in category pdbx_phasing_MAD_shell records R_kraut using acentric data for MAD phasing. attribute R_kraut_centric in category pdbx_phasing_MAD_shell records R_kraut using centric data for MAD phasing. attribute fom in category pdbx_phasing_MAD_shell records the figure of merit for MAD phasing. attribute fom_acentric in category pdbx_phasing_MAD_shell records the figure of merit using acentric data for MAD phasing. attribute fom_centric in category pdbx_phasing_MAD_shell records the figure of merit using centric data for MAD phasing. attribute loc in category pdbx_phasing_MAD_shell records lack of closure for MAD phasing. attribute loc_acentric in category pdbx_phasing_MAD_shell records lack of closure using acentric data for MAD phasing. attribute loc_centric in category pdbx_phasing_MAD_shell records lack of closure using centric data for MAD phasing. attribute loc in category pdbx_phasing_MAD_shell records phasing power for MAD phasing. attribute power_acentric in category pdbx_phasing_MAD_shell records phasing powe using acentric data for MAD phasing. attribute power_centric in category pdbx_phasing_MAD_shell records phasing powe using centric data for MAD phasing. attribute reflns in category pdbx_phasing_MAD_shell records the number of reflections used for MAD phasing. attribute reflns_acentric in category pdbx_phasing_MAD_shell records the number of acentric reflections for MAD phasing. attribute reflns_centric in category pdbx_phasing_MAD_shell records the number of centric reflections for MAD phasing. attribute d_res_high in category pdbx_phasing_MAD_shell records the higher resolution for the shell. attribute d_res_low in category pdbx_phasing_MAD_shell records the lower resolution for the shell. Data items in the PDBX_PHASING_MR category record details about molecular replacement. Example 1 - molecular replacement example from program CNS. <PDBx:pdbx_phasing_MRCategory> <PDBx:pdbx_phasing_MR entry_id="ABC001"> <PDBx:correlation_coeff_Fo_to_Fc>0.586</PDBx:correlation_coeff_Fo_to_Fc> <PDBx:d_res_high_rotation>3.8</PDBx:d_res_high_rotation> <PDBx:d_res_high_translation>4.0</PDBx:d_res_high_translation> <PDBx:d_res_low_rotation>13.0</PDBx:d_res_low_rotation> <PDBx:d_res_low_translation>15.0</PDBx:d_res_low_translation> <PDBx:method_rotation>real-space rotation search</PDBx:method_rotation> <PDBx:method_translation>gerneral using PC-refinement= e2e2</PDBx:method_translation> <PDBx:packing>0.3086</PDBx:packing> <PDBx:reflns_percent_rotation>97.8</PDBx:reflns_percent_rotation> <PDBx:reflns_percent_translation>97.7</PDBx:reflns_percent_translation> <PDBx:sigma_F_rotation>1.0</PDBx:sigma_F_rotation> <PDBx:sigma_F_translation>0</PDBx:sigma_F_translation> </PDBx:pdbx_phasing_MR> </PDBx:pdbx_phasing_MRCategory> The log-likelihood gain after rotation. Read, R.J. (2001). "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57, 1373-1382 The log-likelihood gain after translation. Read, R.J. (2001). "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57, 1373-1382 The value of attribute R_factor in category pdbx_phasing_MR identifies the R factor (defined as uasual) after rotation and translation. The value of attribute R_rigid_body in category pdbx_phasing_MR identifies the R factor for rigid body refinement after rotation and translation.(In general, rigid body refinement has to be carried out after molecular replacement. The value of attribute correlation_coeff_Fo_to_Fc in category pdbx_phasing_MR identifies the correlation between the observed and the calculated structure factor after rotation and translation. The value of attribute correlation_coeff_Io_to_Ic in category pdbx_phasing_MR identifies the correlation between the observed and the calculated intensity (~|F|^2) after rotation and translation. The highest resolution limit used for rigid body refinement after molecular replacement (MR) solution. The value of attribute d_res_high_rotation in category pdbx_phasing_MR identifies the highest resolution used for rotation search. The value of attribute d_res_high_translation in category pdbx_phasing_MR identifies the highest resolution used for translation search. The lowest resolution limit used for rigid body refinement after molecular replacement (MR) solution. The value of attribute d_res_low_rotation in category pdbx_phasing_MR identifies the lowest resolution used for rotation search. The value of attribute d_res_low_translation in category pdbx_phasing_MR identifies the lowest resolution used for translation search. The value of attribute method_rotation in category pdbx_phasing_MR identifies the method used for rotation search. For example, the rotation method may be realspace, fastdirect, or direct. . The value of attribute method_translation in category pdbx_phasing_MR identifies the method used for translation search. For example in CNS, the translation method may be "general" or "phased" with PC refinement target using "fastf2f2" "e2e2" "e1e1" "f2f2" "f1f1" "residual" "vector". . The value of attribute model_details in category pdbx_phasing_MR records the details of model used. For example, the original model can be truncated by deleting side chains, doubtful parts, using the monomer if the original model was an oligomer. The search model may be one domain of a large molecule. What is the pdb IDs. The data set that was treated as the native in this experiment. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. The value of attribute packing in category pdbx_phasing_MR identifies the packing of search model in the unit cell. Too many crystallographic contacts may indicate a bad search. The value of attribute reflns_percent_rotation in category pdbx_phasing_MR identifies the completness of data used for rotation search. The value of attribute reflns_percent_translation in category pdbx_phasing_MR identifies the completness of data used for translation search. The value of attribute sigma_F_rotation in category pdbx_phasing_MR identifies the sigma cut off of structure factor used for rotation search. The value of attribute sigma_F_translation in category pdbx_phasing_MR identifies the sigma cut off of structure factor used for translation search. The value of attribute sigma_I_rotation in category pdbx_phasing_MR identifies the sigma cut off of intensity used for rotation search. The value of attribute sigma_I_translation in category pdbx_phasing_MR identifies the sigma cut off of intensity used for translation search. It is computed by comparing the LLG values from the rotation search with LLG values for a set of random rotations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation. Read, R.J. (2001). "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57, 1373-1382 It is computed by comparing the LLG values from the translation search with LLG values for a set of random translations. The mean and the RMS deviation from the mean are computed from the random set, then the Z-score for a search peak is defined as its LLG minus the mean, all divided by the RMS deviation. Read, R.J. (2001). "Pushing the boundaries of molecular replacement with maximum likelihood." Acta Cryst. D57, 1373-1382 The value of attribute entry_id in category pdbx_phasing_MR identifies the data block. Data items in the PDBX_PHASING_DM category record details about density modification Example 1 - density modification from resolve <PDBx:pdbx_phasing_dmCategory> <PDBx:pdbx_phasing_dm entry_id="ABC001"> <PDBx:fom>0.85</PDBx:fom> <PDBx:fom_acentric>0.85</PDBx:fom_acentric> <PDBx:fom_centric>0.79</PDBx:fom_centric> <PDBx:reflns>12486</PDBx:reflns> <PDBx:reflns_acentric>11351</PDBx:reflns_acentric> <PDBx:reflns_centric>1135</PDBx:reflns_centric> </PDBx:pdbx_phasing_dm> </PDBx:pdbx_phasing_dmCategory> The value of attribute delta_phi_final in category pdbx_phasing_dm identifies phase difference after density modification The value of attribute delta_phi_initial in category pdbx_phasing_dm identifies phase difference before density modification The value of attribute fom in category pdbx_phasing_dm identifies the figure of merit for all the data The value of attribute fom_acentric in category pdbx_phasing_dm identifies the figure of merit for acentric data The value of attribute fom_centric in category pdbx_phasing_dm identifies the figure of merit for acentric data The value of attribute mask_type in category pdbx_phasing_dm identifies the type of mask used for density modification The value of attribute method in category pdbx_phasing_dm identifies the method used for density modification The value of attribute reflns in category pdbx_phasing_dm identifies the number of centric and acentric reflections. The value of attribute reflns_acentric in category pdbx_phasing_dm identifies the number of acentric reflections. The value of attribute reflns_centric in category pdbx_phasing_dm identifies the number of centric reflections. The value of attribute entry_id in category pdbx_phasing_dm identifies the data block. Data items in the PDBX_PHASING_DM_SHELL category record details about density modification in resolution shell. Example 1 - density modification with shells <PDBx:pdbx_phasing_dm_shellCategory> <PDBx:pdbx_phasing_dm_shell d_res_high="7.73" d_res_low="100.00"> <PDBx:delta_phi_final>24.7</PDBx:delta_phi_final> <PDBx:fom>0.879</PDBx:fom> <PDBx:reflns>502</PDBx:reflns> </PDBx:pdbx_phasing_dm_shell> <PDBx:pdbx_phasing_dm_shell d_res_high="6.24" d_res_low="7.73"> <PDBx:delta_phi_final>29.2</PDBx:delta_phi_final> <PDBx:fom>0.857</PDBx:fom> <PDBx:reflns>506</PDBx:reflns> </PDBx:pdbx_phasing_dm_shell> <PDBx:pdbx_phasing_dm_shell d_res_high="5.50" d_res_low="6.24"> <PDBx:delta_phi_final>29.2</PDBx:delta_phi_final> <PDBx:fom>0.838</PDBx:fom> <PDBx:reflns>504</PDBx:reflns> </PDBx:pdbx_phasing_dm_shell> <PDBx:pdbx_phasing_dm_shell d_res_high="5.02" d_res_low="5.50"> <PDBx:delta_phi_final>25.3</PDBx:delta_phi_final> <PDBx:fom>0.851</PDBx:fom> <PDBx:reflns>502</PDBx:reflns> </PDBx:pdbx_phasing_dm_shell> <PDBx:pdbx_phasing_dm_shell d_res_high="4.67" d_res_low="5.02"> <PDBx:delta_phi_final>22.7</PDBx:delta_phi_final> <PDBx:fom>0.831</PDBx:fom> <PDBx:reflns>503</PDBx:reflns> </PDBx:pdbx_phasing_dm_shell> </PDBx:pdbx_phasing_dm_shellCategory> The value of attribute delta_phi_final in category pdbx_phasing_dm_shell identifies phase difference after density modification with resolution shells. The value of attribute delta_phi_initial in category pdbx_phasing_dm_shell identifies phase difference before density modification with resolution shells. The value of attribute fom in category pdbx_phasing_dm_shell identifies the figure of merit for all the data with resolution shells. The value of attribute fom_acentric in category pdbx_phasing_dm_shell identifies the figure of merit for acentric data with resolution shells The value of attribute fom_centric in category pdbx_phasing_dm_shell identifies the figure of merit for centric data with resolution shells. The value of attribute reflns in category pdbx_phasing_dm_shell identifies the number of centric and acentric reflections with resolution shells. The value of attribute reflns_acentric in category pdbx_phasing_dm_shell identifies the number of acentric reflections with resolution shells. The value of attribute reflns_centric in category pdbx_phasing_dm_shell identifies the number of centric reflections with resolution shells. The value of attribute d_res_high in category pdbx_phasing_dm_shell identifies high resolution The value of attribute d_res_low in category pdbx_phasing_dm_shell identifies low resolution Data items in the PDBX_POINT_SYMMETRY category record details about the point symmetry group associated with this entry. Example 1 - <PDBx:pdbx_point_symmetryCategory> <PDBx:pdbx_point_symmetry entry_id="1ABC"> <PDBx:H-M_notation>532</PDBx:H-M_notation> <PDBx:Schoenflies_symbol>I</PDBx:Schoenflies_symbol> </PDBx:pdbx_point_symmetry> </PDBx:pdbx_point_symmetryCategory> The Hermann-Mauguin notation for this point symmetry group. I -> 532 O -> 432 T -> 23 Cn -> n (e.g. C5 -> 5) Dn -> n22 (n even) Dn -> n2 (n odd) The Schoenflies point symmetry symbol. Rotational n-fold C and D point symmetry. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PDBX_POINT_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_POINT_SYMMETRY. Example 1 - <PDBx:pdbx_point_symmetry_depositor_infoCategory> <PDBx:pdbx_point_symmetry_depositor_info entry_id="1ABC"> <PDBx:H-M_notation>532</PDBx:H-M_notation> <PDBx:Schoenflies_symbol>I</PDBx:Schoenflies_symbol> </PDBx:pdbx_point_symmetry_depositor_info> </PDBx:pdbx_point_symmetry_depositor_infoCategory> The Hermann-Mauguin notation for this point symmetry group. I -> 532 O -> 432 T -> 23 Cn -> n (e.g. C5 -> 5) Dn -> n22 (n even) Dn -> n2 (n odd) The Schoenflies point symmetry symbol. Rotational n-fold C and D point symmetry. A flag to indicate that this data is relevant to the current entry This data item is a pointer to attribute id in category entry in the ENTRY category. The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities. Example 1 - based on NDB entry DDFB25 <PDBx:pdbx_poly_seq_schemeCategory> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DC" seq_id="1"> <PDBx:auth_mon_id>DC</PDBx:auth_mon_id> <PDBx:auth_seq_num>1</PDBx:auth_seq_num> <PDBx:ndb_seq_num>1</PDBx:ndb_seq_num> <PDBx:pdb_ins_code xsi:nil="true" /> <PDBx:pdb_mon_id>DC</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>1</PDBx:pdb_seq_num> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DG" seq_id="2"> <PDBx:auth_mon_id>DG</PDBx:auth_mon_id> <PDBx:auth_seq_num>2</PDBx:auth_seq_num> <PDBx:ndb_seq_num>2</PDBx:ndb_seq_num> <PDBx:pdb_ins_code xsi:nil="true" /> <PDBx:pdb_mon_id>DG</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>2</PDBx:pdb_seq_num> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DT" seq_id="3"> <PDBx:auth_mon_id>DT</PDBx:auth_mon_id> <PDBx:auth_seq_num>3</PDBx:auth_seq_num> <PDBx:ndb_seq_num>3</PDBx:ndb_seq_num> <PDBx:pdb_ins_code xsi:nil="true" /> <PDBx:pdb_mon_id>DT</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>3</PDBx:pdb_seq_num> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DA" seq_id="4"> <PDBx:auth_mon_id>DA</PDBx:auth_mon_id> <PDBx:auth_seq_num>4</PDBx:auth_seq_num> <PDBx:ndb_seq_num>4</PDBx:ndb_seq_num> <PDBx:pdb_ins_code xsi:nil="true" /> <PDBx:pdb_mon_id>DA</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>4</PDBx:pdb_seq_num> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DC" seq_id="5"> <PDBx:auth_mon_id>DC</PDBx:auth_mon_id> <PDBx:auth_seq_num>5</PDBx:auth_seq_num> <PDBx:ndb_seq_num>5</PDBx:ndb_seq_num> <PDBx:pdb_ins_code xsi:nil="true" /> <PDBx:pdb_mon_id>DC</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>5</PDBx:pdb_seq_num> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> <PDBx:pdbx_poly_seq_scheme asym_id="A" entity_id="1" mon_id="DG" seq_id="6"> <PDBx:auth_mon_id>DG</PDBx:auth_mon_id> <PDBx:auth_seq_num>6</PDBx:auth_seq_num> <PDBx:ndb_seq_num>6</PDBx:ndb_seq_num> <PDBx:pdb_ins_code xsi:nil="true" /> <PDBx:pdb_mon_id>DG</PDBx:pdb_mon_id> <PDBx:pdb_seq_num>6</PDBx:pdb_seq_num> <PDBx:pdb_strand_id>A</PDBx:pdb_strand_id> </PDBx:pdbx_poly_seq_scheme> </PDBx:pdbx_poly_seq_schemeCategory> Author provided residue identifier. This value may differ from the PDB residue identifier and may not correspond to residue identifier within the coordinate records. Author provided residue number. This value may differ from the PDB residue number and may not correspond to residue numbering within the coordinate records. Pointer to attribute hetero in category entity_poly_seq NDB residue number. PDB insertion code. PDB residue identifier. PDB residue number. PDB strand/chain id. Pointer to attribute label_asym_id in category atom_site. 1 A 2B3 Pointer to attribute id in category entity. Pointer to attribute mon_id in category entity_poly_seq. Pointer to attribute num in category entity_poly_seq Data items in the PDBX_POST_PROCESS_DETAILS identify problems or errors encountered in the post-processing of this entry. <PDBx:pdbx_post_process_detailsCategory> <PDBx:pdbx_post_process_details entry_id="RCSB001"> <PDBx:text> The missing SEQRES record for chain B was added</PDBx:text> </PDBx:pdbx_post_process_details> </PDBx:pdbx_post_process_detailsCategory> Details concerning the standardization of the chemical sequence data in this entry. The text description of changes required to standardize this entry. This should include any errors detected or changes in nomenclature. The value of attribute entry_id in category pdbx_post_process_details identifies the data block. Data items in the PDBX_POST_PROCESS_DETAILS record the status of post-processed entries. <PDBx:pdbx_post_process_statusCategory> <PDBx:pdbx_post_process_status cycle_id="1" entry_id="RCSB001"> <PDBx:date_begin>1998-10-22</PDBx:date_begin> <PDBx:date_end>1998-10-22</PDBx:date_end> <PDBx:details> Fix ligand nomenclature</PDBx:details> </PDBx:pdbx_post_process_status> </PDBx:pdbx_post_process_statusCategory> The name of the annotator. Anke Gelbin The starting date for the current post-processing cycle. 1998-10-22:09:30 The completion date for the current post-processing cycle. 1998-10-22:10:00 A description of the current post-processing cycle. Fixing ligand nomenclature. Identifier for the current cycle of post-processing. 1 for the initial cycle The value of attribute entry_id in category pdbx_post_process_status identifies the data block. Data items in the PDBX_PRD_AUDIT category records the status and tracking information for this molecule. Example 1 - <PDBx:pdbx_prd_auditCategory> <PDBx:pdbx_prd_audit action_type="Create molecule" date="2011-12-01" prd_id="PRD_0000001"> <PDBx:annotator>JY</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_prd_audit> <PDBx:pdbx_prd_audit action_type="Modify sequence" date="2011-12-05" prd_id="PRD_0000001"> <PDBx:annotator>MZ</PDBx:annotator> <PDBx:processing_site>RCSB</PDBx:processing_site> </PDBx:pdbx_prd_audit> </PDBx:pdbx_prd_auditCategory> The initials of the annotator creating of modifying the molecule. JO SJ KB Additional details decribing this change. Revise molecule sequence. An identifier for the wwPDB site creating or modifying the molecule. RCSB PDBe PDBJ BMRB PDBC The action associated with this audit record. The date associated with this audit record. This data item is a pointer to attribute prd_id in category pdbx_reference_molecule in the pdbx_reference_molecule category. This category provides a placeholder for pre-release sequence information. After release this category should be discarded. <PDBx:pdbx_prerelease_seqCategory> <PDBx:pdbx_prerelease_seq entity_id="1"> <PDBx:seq_one_letter_code>GKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD</PDBx:seq_one_letter_code> </PDBx:pdbx_prerelease_seq> <PDBx:pdbx_prerelease_seq entity_id="2"> <PDBx:seq_one_letter_code>HKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNN</PDBx:seq_one_letter_code> </PDBx:pdbx_prerelease_seq> </PDBx:pdbx_prerelease_seqCategory> Chemical sequence expressed as string of one-letter amino acid codes. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD This data item is a pointer to attribute id in category entity in the ENTITY category. Data items in the PDBX_PROTEIN_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated. Example 1 - based on NDB entry PDE001 <PDBx:pdbx_protein_infoCategory> <PDBx:pdbx_protein_info id="1"> <PDBx:name>ECO RI endonuclease</PDBx:name> <PDBx:num_per_asym_unit>1</PDBx:num_per_asym_unit> </PDBx:pdbx_protein_info> </PDBx:pdbx_protein_infoCategory> Name of protein. Number of protein molecules per asymmetric unit. Serial number. Describes the origin of the experimental data used in this entry. Example 1 - <PDBx:pdbx_re_refinementCategory> <PDBx:pdbx_re_refinement entry_id="1ABC"> <PDBx:citation_id>2</PDBx:citation_id> <PDBx:details>Re-refinement of data from entry 1ABC</PDBx:details> </PDBx:pdbx_re_refinement> </PDBx:pdbx_re_refinementCategory> A pointer to attribute id in category citation in category CITATION describing the citation of the entry from from which the experimental data were obtained. Additional details about this re-refinement. The identifier for entry where the experimental data was obtained. Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about the linkages between entities within reference molecules. Example 1 - quinoxaline <PDBx:pdbx_reference_entity_linkCategory> <PDBx:pdbx_reference_entity_link link_id="1" prd_id="PRD_000001"> <PDBx:atom_id_1>N</PDBx:atom_id_1> <PDBx:atom_id_2>C</PDBx:atom_id_2> <PDBx:comp_id_1>DSN</PDBx:comp_id_1> <PDBx:comp_id_2>QUI</PDBx:comp_id_2> <PDBx:component_1>1</PDBx:component_1> <PDBx:component_2>2</PDBx:component_2> <PDBx:entity_seq_num_1>1</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2 xsi:nil="true" /> <PDBx:link_class>PN</PDBx:link_class> <PDBx:ref_entity_id_1>1</PDBx:ref_entity_id_1> <PDBx:ref_entity_id_2>2</PDBx:ref_entity_id_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_link> <PDBx:pdbx_reference_entity_link link_id="2" prd_id="PRD_000001"> <PDBx:atom_id_1>N</PDBx:atom_id_1> <PDBx:atom_id_2>C</PDBx:atom_id_2> <PDBx:comp_id_1>DSN</PDBx:comp_id_1> <PDBx:comp_id_2>QUI</PDBx:comp_id_2> <PDBx:component_1>1</PDBx:component_1> <PDBx:component_2>3</PDBx:component_2> <PDBx:entity_seq_num_1>5</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2 xsi:nil="true" /> <PDBx:link_class>PN</PDBx:link_class> <PDBx:ref_entity_id_1>1</PDBx:ref_entity_id_1> <PDBx:ref_entity_id_2>3</PDBx:ref_entity_id_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_link> </PDBx:pdbx_reference_entity_linkCategory> The atom identifier/name in the first of the two entities containing the linkage. The atom identifier/name in the second of the two entities containing the linkage. The component identifier in the first of the two entities containing the linkage. For polymer entities, this data item is a pointer to attribute mon_id in category pdbx_reference_entity_poly_seq in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. For non-polymer entities, this data item is a pointer to attribute chem_comp_id in category pdbx_reference_entity_nonpoly in the PDBX_REFERENCE_ENTITY_NONPOLY category. The component identifier in the second of the two entities containing the linkage. For polymer entities, this data item is a pointer to attribute mon_id in category pdbx_reference_entity_poly_seq in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. For non-polymer entities, this data item is a pointer to attribute chem_comp_id in category pdbx_reference_entity_nonpoly in the PDBX_REFERENCE_ENTITY_NONPOLY category. The entity component identifier for the first of two entities containing the linkage. The entity component identifier for the second of two entities containing the linkage. A description of special aspects of a linkage between chemical components in the structure. For a polymer entity, the sequence number in the first of the two entities containing the linkage. This data item is a pointer to attribute num in category pdbx_reference_entity_poly_seq in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. For a polymer entity, the sequence number in the second of the two entities containing the linkage. This data item is a pointer to attribute num in category pdbx_reference_entity_poly_seq in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. A code indicating the entity types involved in the linkage. The residue number for the first of two entities containing the linkage. The residue number for the second of two entities containing the linkage. The reference entity id of the first of the two entities joined by the linkage. This data item is a pointer to attribute ref_entity_id in category pdbx_reference_entity_list in the PDBX_REFERENCE_ENTITY_LIST category. The reference entity id of the second of the two entities joined by the linkage. This data item is a pointer to attribute ref_entity_id in category pdbx_reference_entity_list in the PDBX_REFERENCE_ENTITY_LIST category. The bond order target for the chemical linkage. The value of attribute link_id in category pdbx_reference_entity_link uniquely identifies linkages between entities with a molecule. The value of attribute prd_id in category pdbx_reference_entity_link is a reference attribute prd_id in category pdbx_reference_entity_list in the PDBX_REFERENCE_ENTITY_LIST category. Data items in the PDBX_REFERENCE_ENTITY_LIST category record the list of entities within each reference molecule. Example: 1 <PDBx:pdbx_reference_entity_listCategory> <PDBx:pdbx_reference_entity_list component_id="1" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:details>PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 8</PDBx:details> <PDBx:type>polymer</PDBx:type> </PDBx:pdbx_reference_entity_list> <PDBx:pdbx_reference_entity_list component_id="2" prd_id="PRD_000001" ref_entity_id="2"> <PDBx:details>QUINALDIC ACID CHROMOPHORE</PDBx:details> <PDBx:type>non-polymer</PDBx:type> </PDBx:pdbx_reference_entity_list> <PDBx:pdbx_reference_entity_list component_id="3" prd_id="PRD_000001" ref_entity_id="3"> <PDBx:details>QUINALDIC ACID CHROMOPHORE</PDBx:details> <PDBx:type>non-polymer</PDBx:type> </PDBx:pdbx_reference_entity_list> </PDBx:pdbx_reference_entity_listCategory> Additional details about this entity. Defines the polymer characteristic of the entity. polymer non-polymer branched The component number of this entity within the molecule. The value of attribute prd_id in category pdbx_reference_entity_list is a reference attribute prd_id in category pdbx_reference_molecule in the PDBX_REFERENCE_MOLECULE category. The value of attribute ref_entity_id in category pdbx_reference_entity_list is a unique identifier the a constituent entity within this reference molecule. Data items in the PDBX_REFERENCE_ENTITY_NONPOLY category record the list of entities within each reference molecule. Example: 1 <PDBx:pdbx_reference_entity_nonpolyCategory> <PDBx:pdbx_reference_entity_nonpoly prd_id="PRD_000004" ref_entity_id="2"> <PDBx:chem_comp_id>QUI</PDBx:chem_comp_id> <PDBx:name>2-CARBOXYQUINOXALINE</PDBx:name> </PDBx:pdbx_reference_entity_nonpoly> </PDBx:pdbx_reference_entity_nonpolyCategory> For non-polymer entities, the identifier corresponding to the chemical definition for the molecule. 0Z3 CD9 Additional details about this entity. A name of the non-polymer entity. 2-CARBOXYQUINOXALINE The value of attribute prd_id in category pdbx_reference_entity_nonpoly is a reference attribute prd_id in category pdbx_reference_entity_list in the PDBX_REFERENCE_ENTITY_LIST category. The value of attribute ref_entity_id in category pdbx_reference_entity_nonpoly is a reference to attribute ref_entity_id in category pdbx_reference_entity_list in PDBX_REFERENCE_ENTITY_LIST category. Data items in the PDBX_REFERENCE_ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features. Example: 1 Actinomycin <PDBx:pdbx_reference_entity_polyCategory> <PDBx:pdbx_reference_entity_poly prd_id="PRD_000001" ref_entity_id="1"> <PDBx:db_code>NOR00228</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_poly> <PDBx:pdbx_reference_entity_poly prd_id="PRD_000006" ref_entity_id="2"> <PDBx:db_name>Semi-synthetic</PDBx:db_name> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_poly> <PDBx:pdbx_reference_entity_poly prd_id="PRD_000007" ref_entity_id="3"> <PDBx:db_code>NOR00232</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_poly> <PDBx:pdbx_reference_entity_poly prd_id="PRD_000009" ref_entity_id="4"> <PDBx:db_code>NOR00237</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_poly> <PDBx:pdbx_reference_entity_poly prd_id="PRD_000010" ref_entity_id="5"> <PDBx:db_name>Semi-synthetic</PDBx:db_name> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_poly> <PDBx:pdbx_reference_entity_poly prd_id="PRD_000011" ref_entity_id="6"> <PDBx:db_name>Semi-synthetic</PDBx:db_name> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_poly> </PDBx:pdbx_reference_entity_polyCategory> The database code for this source information The database name for this source information The type of the polymer. peptide-like The value of attribute prd_id in category pdbx_reference_entity_poly is a reference attribute prd_id in category pdbx_reference_entity_list in the PDBX_REFERENCE_ENTITY_LIST category. The value of attribute ref_entity_id in category pdbx_reference_entity_poly is a reference to attribute ref_entity_id in category pdbx_reference_entity_list in PDBX_REFERENCE_ENTITY_LIST category. Data items in the PDBX_REFERENCE_ENTITY_POLY_LINK category give details about polymer linkages including both standard and non-standard linkages between polymer componnents. Example 1 - <PDBx:pdbx_reference_entity_poly_linkCategory> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="1" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>DSN</PDBx:comp_id_1> <PDBx:comp_id_2>ALA</PDBx:comp_id_2> <PDBx:entity_seq_num_1>1</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>2</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="2" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>ALA</PDBx:comp_id_1> <PDBx:comp_id_2>N2C</PDBx:comp_id_2> <PDBx:entity_seq_num_1>2</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>3</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="3" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>ALA</PDBx:comp_id_1> <PDBx:comp_id_2>N2C</PDBx:comp_id_2> <PDBx:entity_seq_num_1>2</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>3</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="4" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>ALA</PDBx:comp_id_1> <PDBx:comp_id_2>NCY</PDBx:comp_id_2> <PDBx:entity_seq_num_1>2</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>3</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="5" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>N2C</PDBx:comp_id_1> <PDBx:comp_id_2>MVA</PDBx:comp_id_2> <PDBx:entity_seq_num_1>3</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>4</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="6" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>NCY</PDBx:comp_id_1> <PDBx:comp_id_2>MVA</PDBx:comp_id_2> <PDBx:entity_seq_num_1>3</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>4</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="7" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>OG</PDBx:atom_id_2> <PDBx:comp_id_1>MVA</PDBx:comp_id_1> <PDBx:comp_id_2>DSN</PDBx:comp_id_2> <PDBx:entity_seq_num_1>4</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>5</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="8" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>DSN</PDBx:comp_id_1> <PDBx:comp_id_2>ALA</PDBx:comp_id_2> <PDBx:entity_seq_num_1>5</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>6</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="8" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>ALA</PDBx:comp_id_1> <PDBx:comp_id_2>NCY</PDBx:comp_id_2> <PDBx:entity_seq_num_1>6</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>7</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="9" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>ALA</PDBx:comp_id_1> <PDBx:comp_id_2>N2C</PDBx:comp_id_2> <PDBx:entity_seq_num_1>6</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>7</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="8" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>NCY</PDBx:comp_id_1> <PDBx:comp_id_2>MVA</PDBx:comp_id_2> <PDBx:entity_seq_num_1>7</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>8</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> <PDBx:pdbx_reference_entity_poly_link component_id="1" link_id="9" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:atom_id_1>C</PDBx:atom_id_1> <PDBx:atom_id_2>N</PDBx:atom_id_2> <PDBx:comp_id_1>N2C</PDBx:comp_id_1> <PDBx:comp_id_2>MVZ</PDBx:comp_id_2> <PDBx:entity_seq_num_1>7</PDBx:entity_seq_num_1> <PDBx:entity_seq_num_2>8</PDBx:entity_seq_num_2> <PDBx:value_order>single</PDBx:value_order> </PDBx:pdbx_reference_entity_poly_link> </PDBx:pdbx_reference_entity_poly_linkCategory> The atom identifier/name in the first of the two components making the linkage. The atom identifier/name in the second of the two components making the linkage. The component identifier in the first of the two components making the linkage. This data item is a pointer to attribute mon_id in category pdbx_reference_entity_poly_seq in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. The component identifier in the second of the two components making the linkage. This data item is a pointer to attribute mon_id in category pdbx_reference_entity_poly_seq in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. A description of special aspects of this linkage. For a polymer entity, the sequence number in the first of the two components making the linkage. This data item is a pointer to attribute num in category pdbx_reference_entity_poly_seq in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. For a polymer entity, the sequence number in the second of the two components making the linkage. This data item is a pointer to attribute num in category pdbx_reference_entity_poly_seq in the PDBX_REFERENCE_ENTITY_POLY_SEQ category. The residue insertion code for the first of the two components making the non-standard linkage. The residue insertion code for the second of the two components making the non-standard linkage. The bond order target for the non-standard linkage. The entity component identifier entity containing the linkage. The value of attribute link_id in category pdbx_reference_entity_poly_link uniquely identifies a linkage within a polymer entity. The value of attribute prd_id in category pdbx_reference_entity_poly_link is a reference attribute prd_id in category pdbx_reference_entity_list in the PDBX_REFERENCE_ENTITY_POLY category. The reference entity id of the polymer entity containing the linkage. This data item is a pointer to attribute ref_entity_id in category pdbx_reference_entity_poly in the PDBX_REFERENCE_ENTITY_POLY category. Data items in the PDBX_REFERENCE_ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Example: 1 Actinomycin <PDBx:pdbx_reference_entity_poly_seqCategory> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="THR" num="1" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>THR</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="DVA" num="2" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>VAL</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="PRO" num="3" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>PRO</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="SAR" num="4" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>GLY</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="MVA" num="5" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>VAL</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="PXZ" num="6" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id xsi:nil="true" /> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="THR" num="7" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>THR</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="DVA" num="8" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>VAL</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="PRO" num="9" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>PRO</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="SAR" num="10" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>GLY</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> <PDBx:pdbx_reference_entity_poly_seq hetero="N" mon_id="MVA" num="11" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:observed>Y</PDBx:observed> <PDBx:parent_mon_id>VAL</PDBx:parent_mon_id> </PDBx:pdbx_reference_entity_poly_seq> </PDBx:pdbx_reference_entity_poly_seqCategory> A flag to indicate that this monomer is observed in the instance example. Y This data item is the chemical component identifier for the parent component corresponding to this monomer. A flag to indicate that sequence heterogeneity at this monomer position. N This data item is the chemical component identifier of monomer. The value of attribute num in category pdbx_reference_entity_poly_seq must uniquely and sequentially identify a record in the PDBX_REFERENCE_ENTITY_POLY_SEQ list. This value is conforms to author numbering conventions and does not map directly to the numbering conventions used for attribute num in category entity_poly_seq. The value of attribute prd_id in category pdbx_reference_entity_poly_seq is a reference attribute prd_id in category pdbx_reference_entity_poly in the PDBX_REFERENCE_ENTITY_POLY category. The value of attribute ref_entity_id in category pdbx_reference_entity_poly_seq is a reference to attribute ref_entity_id in category pdbx_reference_entity_poly in PDBX_REFERENCE_ENTITY_POLY category. Additional features associated with the reference entity. Example 1 - Actinomycin <PDBx:pdbx_reference_entity_sequenceCategory> <PDBx:pdbx_reference_entity_sequence prd_id="PRD_000001" ref_entity_id="1"> <PDBx:NRP_flag>Y</PDBx:NRP_flag> <PDBx:one_letter_codes>TVPGVXTVPGV</PDBx:one_letter_codes> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_sequence> <PDBx:pdbx_reference_entity_sequence prd_id="PRD_000006" ref_entity_id="2"> <PDBx:NRP_flag>Y</PDBx:NRP_flag> <PDBx:one_letter_codes>TVPGVXTVPGV</PDBx:one_letter_codes> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_sequence> <PDBx:pdbx_reference_entity_sequence prd_id="PRD_000007" ref_entity_id="3"> <PDBx:NRP_flag>Y</PDBx:NRP_flag> <PDBx:one_letter_codes>TVPGVXTVPGV</PDBx:one_letter_codes> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_sequence> <PDBx:pdbx_reference_entity_sequence prd_id="PRD_000009" ref_entity_id="4"> <PDBx:NRP_flag>Y</PDBx:NRP_flag> <PDBx:one_letter_codes>TVPGVXTVPGV</PDBx:one_letter_codes> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_sequence> <PDBx:pdbx_reference_entity_sequence prd_id="PRD_000010" ref_entity_id="5"> <PDBx:NRP_flag>Y</PDBx:NRP_flag> <PDBx:one_letter_codes>TVPGVXTVPGV</PDBx:one_letter_codes> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_sequence> <PDBx:pdbx_reference_entity_sequence prd_id="PRD_000011" ref_entity_id="6"> <PDBx:NRP_flag>Y</PDBx:NRP_flag> <PDBx:one_letter_codes>TVPGVXTVPGV</PDBx:one_letter_codes> <PDBx:type>peptide-like</PDBx:type> </PDBx:pdbx_reference_entity_sequence> </PDBx:pdbx_reference_entity_sequenceCategory> A flag to indicate a non-ribosomal entity. Y The one-letter-code sequence for this entity. Non-standard monomers are represented as 'X'. The monomer type for the sequence. peptide-like saccharide The value of attribute prd_id in category pdbx_reference_entity_sequence is a reference attribute prd_id in category pdbx_reference_entity_list in the PDBX_REFERENCE_ENTITY_LIST category. The value of attribute ref_entity_id in category pdbx_reference_entity_sequence is a reference to attribute ref_entity_id in category pdbx_reference_entity_list in PDBX_REFERENCE_ENTITY_LIST category. Data items in the PDBX_REFERENCE_ENTITY_SRC_NAT category record details of the source from which the entity was obtained. Example 1 - Actinomycin <PDBx:pdbx_reference_entity_src_natCategory> <PDBx:pdbx_reference_entity_src_nat ordinal="1" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:db_code>C06770</PDBx:db_code> <PDBx:db_name>KEGG</PDBx:db_name> <PDBx:organism_scientific>Streptomyces parvulus</PDBx:organism_scientific> <PDBx:source>KEGG</PDBx:source> <PDBx:taxid>146923</PDBx:taxid> </PDBx:pdbx_reference_entity_src_nat> <PDBx:pdbx_reference_entity_src_nat ordinal="2" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:db_code>NOR00228</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:organism_scientific>Streptomyces anulatus</PDBx:organism_scientific> <PDBx:source>Norine</PDBx:source> <PDBx:taxid>1892</PDBx:taxid> </PDBx:pdbx_reference_entity_src_nat> <PDBx:pdbx_reference_entity_src_nat ordinal="3" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:db_code>NOR00228</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:organism_scientific>Streptomyces antibioticus</PDBx:organism_scientific> <PDBx:source>Norine</PDBx:source> <PDBx:taxid>1890</PDBx:taxid> </PDBx:pdbx_reference_entity_src_nat> <PDBx:pdbx_reference_entity_src_nat ordinal="4" prd_id="PRD_000001" ref_entity_id="1"> <PDBx:db_code>NOR00228</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:organism_scientific>Streptomyces parvulus</PDBx:organism_scientific> <PDBx:source>Norine</PDBx:source> <PDBx:taxid>146923</PDBx:taxid> </PDBx:pdbx_reference_entity_src_nat> <PDBx:pdbx_reference_entity_src_nat ordinal="5" prd_id="PRD_000002" ref_entity_id="2"> <PDBx:db_code>NOR00228</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:organism_scientific>Streptomyces chrysomallus</PDBx:organism_scientific> <PDBx:source>Norine</PDBx:source> <PDBx:taxid>1892</PDBx:taxid> </PDBx:pdbx_reference_entity_src_nat> <PDBx:pdbx_reference_entity_src_nat ordinal="6" prd_id="PRD_000003" ref_entity_id="3"> <PDBx:db_code>NOR00233</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:organism_scientific>Streptomyces chrysomallus</PDBx:organism_scientific> <PDBx:source>Norine</PDBx:source> <PDBx:taxid>1892</PDBx:taxid> </PDBx:pdbx_reference_entity_src_nat> <PDBx:pdbx_reference_entity_src_nat ordinal="7" prd_id="PRD_000003" ref_entity_id="3"> <PDBx:db_code>NOR00233</PDBx:db_code> <PDBx:db_name>Norine</PDBx:db_name> <PDBx:organism_scientific>Streptomyces sp.</PDBx:organism_scientific> <PDBx:source>Norine</PDBx:source> <PDBx:taxid>1931</PDBx:taxid> </PDBx:pdbx_reference_entity_src_nat> </PDBx:pdbx_reference_entity_src_natCategory> The Americal Tissue Culture Collection code for organism from which the entity was isolated. The database code for this source information The database name for this source information The scientific name of the organism from which the entity was isolated. Mus musculus The data source for this information. A identifier within the data source for this information. The strain of the organism from which the entity was isolated. DH5a BMH 71-18 The NCBI TaxId of the organism from which the entity was isolated. The value of attribute ordinal in category pdbx_reference_entity_src_nat distinguishes source details for this entity. The value of attribute prd_id in category pdbx_reference_entity_src_nat is a reference attribute prd_id in category pdbx_reference_entity_list in the PDBX_REFERENCE_ENTITY_LIST category. The value of attribute ref_entity_id in category pdbx_reference_entity_src_nat is a reference to attribute ref_entity_id in category pdbx_reference_entity_list in PDBX_REFERENCE_ENTITY_LIST category. Data items in the PDBX_REFERENCE_ENTITY_SUBCOMPONENTS category records subcomponent sequence from which this entity could be built. Example: 1 0G6 <PDBx:pdbx_reference_entity_subcomponentsCategory> <PDBx:pdbx_reference_entity_subcomponents prd_id="PRD_000001" seq="DPN PRO ARG 0QE"> <PDBx:chem_comp_id>0G6</PDBx:chem_comp_id> </PDBx:pdbx_reference_entity_subcomponents> </PDBx:pdbx_reference_entity_subcomponentsCategory> For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule. 0Z3 CD9 The value of attribute prd_id in category pdbx_reference_entity_subcomponents is a reference attribute prd_id in category pdbx_reference_molecule in the PDBX_REFERENCE_MOLECULE category. The subcomponent sequence for the entity. ACE DLY GLY DAL DCY DAS DTY DPR DGL DTR DGN DTR DLE DCY DAL DAL NH2 Data items in the pdbx_reference_linked_entity category describe common observed interaction patterns within linked entities. Example 1 - <PDBx:pdbx_reference_linked_entityCategory> <PDBx:pdbx_reference_linked_entity id="0"> <PDBx:class>N-linked-glycan</PDBx:class> <PDBx:link_from_entity_type>polysaccharide</PDBx:link_from_entity_type> <PDBx:link_to_comp_id>ASN</PDBx:link_to_comp_id> <PDBx:link_to_entity_type>polypeptide</PDBx:link_to_entity_type> <PDBx:name>basic</PDBx:name> <PDBx:taxonomy_class xsi:nil="true" /> <PDBx:taxonomy_id xsi:nil="true" /> </PDBx:pdbx_reference_linked_entity> <PDBx:pdbx_reference_linked_entity id="1"> <PDBx:class>N-linked-glycan</PDBx:class> <PDBx:link_from_entity_type>polysaccharide</PDBx:link_from_entity_type> <PDBx:link_to_comp_id>ASN</PDBx:link_to_comp_id> <PDBx:link_to_entity_type>polypeptide</PDBx:link_to_entity_type> <PDBx:name>high-mannose simple</PDBx:name> <PDBx:taxonomy_class xsi:nil="true" /> <PDBx:taxonomy_id xsi:nil="true" /> </PDBx:pdbx_reference_linked_entity> <PDBx:pdbx_reference_linked_entity id="2"> <PDBx:class>N-linked-glycan</PDBx:class> <PDBx:link_from_entity_type>polysaccharide</PDBx:link_from_entity_type> <PDBx:link_to_comp_id>ASN</PDBx:link_to_comp_id> <PDBx:link_to_entity_type>polypeptide</PDBx:link_to_entity_type> <PDBx:name>high-mannose</PDBx:name> <PDBx:taxonomy_class xsi:nil="true" /> <PDBx:taxonomy_id xsi:nil="true" /> </PDBx:pdbx_reference_linked_entity> <PDBx:pdbx_reference_linked_entity id="3"> <PDBx:class>N-linked-glycan</PDBx:class> <PDBx:link_from_entity_type>polysaccharide</PDBx:link_from_entity_type> <PDBx:link_to_comp_id>ASN</PDBx:link_to_comp_id> <PDBx:link_to_entity_type>polypeptide</PDBx:link_to_entity_type> <PDBx:name>hybrid simple</PDBx:name> <PDBx:taxonomy_class xsi:nil="true" /> <PDBx:taxonomy_id xsi:nil="true" /> </PDBx:pdbx_reference_linked_entity> <PDBx:pdbx_reference_linked_entity id="4"> <PDBx:class>N-linked-glycan</PDBx:class> <PDBx:link_from_entity_type>polysaccharide</PDBx:link_from_entity_type> <PDBx:link_to_comp_id>ASN</PDBx:link_to_comp_id> <PDBx:link_to_entity_type>polypeptide</PDBx:link_to_entity_type> <PDBx:name>hybrid</PDBx:name> <PDBx:taxonomy_class xsi:nil="true" /> <PDBx:taxonomy_id xsi:nil="true" /> </PDBx:pdbx_reference_linked_entity> <PDBx:pdbx_reference_linked_entity id="5"> <PDBx:class>N-linked-glycan</PDBx:class> <PDBx:link_from_entity_type>polysaccharide</PDBx:link_from_entity_type> <PDBx:link_to_comp_id>ASN</PDBx:link_to_comp_id> <PDBx:link_to_entity_type>polypeptide</PDBx:link_to_entity_type> <PDBx:name>complex</PDBx:name> <PDBx:taxonomy_class>Mammalia</PDBx:taxonomy_class> <PDBx:taxonomy_id>40674</PDBx:taxonomy_id> </PDBx:pdbx_reference_linked_entity> </PDBx:pdbx_reference_linked_entityCategory> Broadly classifies of this linked entity example. The polymer linking type of the second partner entity in example linkage. The component identifer for the component in the first partner of the example linkage. The polymer linking type of the first partner entity in example linkage. The name of the linked entity example. high mannose basic hybrid hybrid simple The NCBI taxonomy classification of the organism for this linked entity example. Archaea Bacteria Eukaryota Embryophyta Fungi Metazoa Vertebrata Mammalia Rodentia Primates The NCBI taxonomy identifier of the organism for the linked entity example. The value of attribute id in category pdbx_reference_linked_entity uniquely identifies examples in the list of observed linking patterns. Data items in the pdbx_reference_linked_entity_comp_link category enumerate inter-entity linkages between the components of common observed interaction patterns described in the pdbx_reference_linked_entity category. Example 1 - <PDBx:pdbx_reference_linked_entity_comp_linkCategory> <PDBx:pdbx_reference_linked_entity_comp_link link_id="1" linked_entity_id="0"> <PDBx:atom_id_1>O4</PDBx:atom_id_1> <PDBx:atom_id_2>C1</PDBx:atom_id_2> <PDBx:atom_stereo_config_1>N</PDBx:atom_stereo_config_1> <PDBx:atom_stereo_config_2>R</PDBx:atom_stereo_config_2> <PDBx:comp_id_1>NAG</PDBx:comp_id_1> <PDBx:comp_id_2>NAG</PDBx:comp_id_2> <PDBx:details>beta 1--&gt;4</PDBx:details> <PDBx:leaving_atom_id_1 xsi:nil="true" /> <PDBx:leaving_atom_id_2>O1</PDBx:leaving_atom_id_2> <PDBx:list_id_1>1</PDBx:list_id_1> <PDBx:list_id_2>2</PDBx:list_id_2> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_comp_link> <PDBx:pdbx_reference_linked_entity_comp_link link_id="2" linked_entity_id="0"> <PDBx:atom_id_1>O4</PDBx:atom_id_1> <PDBx:atom_id_2>C1</PDBx:atom_id_2> <PDBx:atom_stereo_config_1>N</PDBx:atom_stereo_config_1> <PDBx:atom_stereo_config_2>S</PDBx:atom_stereo_config_2> <PDBx:comp_id_1>NAG</PDBx:comp_id_1> <PDBx:comp_id_2>MAN</PDBx:comp_id_2> <PDBx:details>beta 1--&gt;4</PDBx:details> <PDBx:leaving_atom_id_1 xsi:nil="true" /> <PDBx:leaving_atom_id_2>O1</PDBx:leaving_atom_id_2> <PDBx:list_id_1>2</PDBx:list_id_1> <PDBx:list_id_2>3</PDBx:list_id_2> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_comp_link> <PDBx:pdbx_reference_linked_entity_comp_link link_id="3" linked_entity_id="0"> <PDBx:atom_id_1>O3</PDBx:atom_id_1> <PDBx:atom_id_2>C1</PDBx:atom_id_2> <PDBx:atom_stereo_config_1>N</PDBx:atom_stereo_config_1> <PDBx:atom_stereo_config_2>S</PDBx:atom_stereo_config_2> <PDBx:comp_id_1>MAN</PDBx:comp_id_1> <PDBx:comp_id_2>MAN</PDBx:comp_id_2> <PDBx:details>alpha 1--&gt;3</PDBx:details> <PDBx:leaving_atom_id_1 xsi:nil="true" /> <PDBx:leaving_atom_id_2>O1</PDBx:leaving_atom_id_2> <PDBx:list_id_1>3</PDBx:list_id_1> <PDBx:list_id_2>4</PDBx:list_id_2> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_comp_link> <PDBx:pdbx_reference_linked_entity_comp_link link_id="4" linked_entity_id="0"> <PDBx:atom_id_1>O6</PDBx:atom_id_1> <PDBx:atom_id_2>C1</PDBx:atom_id_2> <PDBx:atom_stereo_config_1>N</PDBx:atom_stereo_config_1> <PDBx:atom_stereo_config_2>S</PDBx:atom_stereo_config_2> <PDBx:comp_id_1>MAN</PDBx:comp_id_1> <PDBx:comp_id_2>MAN</PDBx:comp_id_2> <PDBx:details>alpha 1--&gt;6</PDBx:details> <PDBx:leaving_atom_id_1 xsi:nil="true" /> <PDBx:leaving_atom_id_2>O1</PDBx:leaving_atom_id_2> <PDBx:list_id_1>3</PDBx:list_id_1> <PDBx:list_id_2>5</PDBx:list_id_2> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_comp_link> </PDBx:pdbx_reference_linked_entity_comp_linkCategory> The atom identifier/name in the first of the two constituents containing the linkage. The atom identifier/name in the second of the two constituents containing the linkage. The chiral configuration of the first atom making the linkage. The chiral configuration of the second atom making the linkage. The component identifier in the first of the two constituents containing the linkage. The component identifier in the second of the two constituents containing the linkage. A description of special aspects of a linkage between these constituents in this linked entity. The leaving atom identifier/name bonded to the first atom making the linkage. The leaving atom identifier/name bonded to the second atom making the linkage. The value of attribute list_id_1 in category pdbx_reference_linked_entity_comp_link is a reference attribute list_id in category pdbx_reference_linked_entity_comp_list in the pdbx_reference_linked_entity_comp_list category. The value of attribute list_id_2 in category pdbx_reference_linked_entity_comp_link is a reference attribute list_id in category pdbx_reference_linked_entity_comp_list in the pdbx_reference_linked_entity_comp_list category. The bond order target for the chemical linkage. The value of attribute link_id in category pdbx_reference_linked_entity_comp_link uniquely identifies linkages within the linked entity. The value of attribute linked_entity_id in category pdbx_reference_linked_entity_comp_link is a reference attribute linked_entity_id in category pdbx_reference_linked_entity_comp_list in the pdbx_reference_linked_entity_comp_list category. Data items in the pdbx_reference_linked_entity_comp_list category lists the constituents of common observed interaction patterns described in the pdbx_reference_linked_entity category. Example 1 - <PDBx:pdbx_reference_linked_entity_comp_listCategory> <PDBx:pdbx_reference_linked_entity_comp_list linked_entity_id="0" list_id="1"> <PDBx:comp_id>NAG</PDBx:comp_id> <PDBx:name>N-acetyl glucosamine</PDBx:name> </PDBx:pdbx_reference_linked_entity_comp_list> <PDBx:pdbx_reference_linked_entity_comp_list linked_entity_id="0" list_id="2"> <PDBx:comp_id>NAG</PDBx:comp_id> <PDBx:name>N-acetyl glucosamine</PDBx:name> </PDBx:pdbx_reference_linked_entity_comp_list> <PDBx:pdbx_reference_linked_entity_comp_list linked_entity_id="0" list_id="3"> <PDBx:comp_id>MAN</PDBx:comp_id> <PDBx:name>Mannose</PDBx:name> </PDBx:pdbx_reference_linked_entity_comp_list> <PDBx:pdbx_reference_linked_entity_comp_list linked_entity_id="0" list_id="4"> <PDBx:comp_id>MAN</PDBx:comp_id> <PDBx:name>Mannose</PDBx:name> </PDBx:pdbx_reference_linked_entity_comp_list> <PDBx:pdbx_reference_linked_entity_comp_list linked_entity_id="0" list_id="5"> <PDBx:comp_id>MAN</PDBx:comp_id> <PDBx:name>Mannose</PDBx:name> </PDBx:pdbx_reference_linked_entity_comp_list> </PDBx:pdbx_reference_linked_entity_comp_listCategory> The component identifer for the constituent within the linked entity.. The name of the constituent withing the linked entity. protein-Asparagine N-acetyl glucosamine This data item is a pointer to attribute id in category pdbx_reference_linked_entity in the pdbx_reference_linked_entity category. This data item uniquely identifies a constituent of with the linked entity. Data items in the pdbx_reference_linked_entity_link category enumerate linkages between the entities in common observed interaction patterns described in the pdbx_reference_linked_entity category. Example 1 - <PDBx:pdbx_reference_linked_entity_linkCategory> <PDBx:pdbx_reference_linked_entity_link link_id="1" linked_entity_id="0"> <PDBx:from_atom_id>C1</PDBx:from_atom_id> <PDBx:from_atom_stereo_config>R</PDBx:from_atom_stereo_config> <PDBx:from_comp_id>NAG</PDBx:from_comp_id> <PDBx:from_leaving_atom_id>O1</PDBx:from_leaving_atom_id> <PDBx:from_list_id>1</PDBx:from_list_id> <PDBx:to_atom_id>ND2</PDBx:to_atom_id> <PDBx:to_comp_id>ASN</PDBx:to_comp_id> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_link> <PDBx:pdbx_reference_linked_entity_link link_id="1" linked_entity_id="1"> <PDBx:from_atom_id>C1</PDBx:from_atom_id> <PDBx:from_atom_stereo_config>R</PDBx:from_atom_stereo_config> <PDBx:from_comp_id>NAG</PDBx:from_comp_id> <PDBx:from_leaving_atom_id>O1</PDBx:from_leaving_atom_id> <PDBx:from_list_id>1</PDBx:from_list_id> <PDBx:to_atom_id>ND2</PDBx:to_atom_id> <PDBx:to_comp_id>ASN</PDBx:to_comp_id> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_link> <PDBx:pdbx_reference_linked_entity_link link_id="1" linked_entity_id="2"> <PDBx:from_atom_id>C1</PDBx:from_atom_id> <PDBx:from_atom_stereo_config>R</PDBx:from_atom_stereo_config> <PDBx:from_comp_id>NAG</PDBx:from_comp_id> <PDBx:from_leaving_atom_id>O1</PDBx:from_leaving_atom_id> <PDBx:from_list_id>1</PDBx:from_list_id> <PDBx:to_atom_id>ND2</PDBx:to_atom_id> <PDBx:to_comp_id>ASN</PDBx:to_comp_id> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_link> <PDBx:pdbx_reference_linked_entity_link link_id="1" linked_entity_id="3"> <PDBx:from_atom_id>C1</PDBx:from_atom_id> <PDBx:from_atom_stereo_config>R</PDBx:from_atom_stereo_config> <PDBx:from_comp_id>NAG</PDBx:from_comp_id> <PDBx:from_leaving_atom_id>O1</PDBx:from_leaving_atom_id> <PDBx:from_list_id>1</PDBx:from_list_id> <PDBx:to_atom_id>ND2</PDBx:to_atom_id> <PDBx:to_comp_id>ASN</PDBx:to_comp_id> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_link> <PDBx:pdbx_reference_linked_entity_link link_id="1" linked_entity_id="4"> <PDBx:from_atom_id>C1</PDBx:from_atom_id> <PDBx:from_atom_stereo_config>R</PDBx:from_atom_stereo_config> <PDBx:from_comp_id>NAG</PDBx:from_comp_id> <PDBx:from_leaving_atom_id>O1</PDBx:from_leaving_atom_id> <PDBx:from_list_id>1</PDBx:from_list_id> <PDBx:to_atom_id>ND2</PDBx:to_atom_id> <PDBx:to_comp_id>ASN</PDBx:to_comp_id> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_link> <PDBx:pdbx_reference_linked_entity_link link_id="1" linked_entity_id="5"> <PDBx:from_atom_id>C1</PDBx:from_atom_id> <PDBx:from_atom_stereo_config>R</PDBx:from_atom_stereo_config> <PDBx:from_comp_id>NAG</PDBx:from_comp_id> <PDBx:from_leaving_atom_id>O1</PDBx:from_leaving_atom_id> <PDBx:from_list_id>1</PDBx:from_list_id> <PDBx:to_atom_id>ND2</PDBx:to_atom_id> <PDBx:to_comp_id>ASN</PDBx:to_comp_id> <PDBx:value_order>sing</PDBx:value_order> </PDBx:pdbx_reference_linked_entity_link> </PDBx:pdbx_reference_linked_entity_linkCategory> A description of special aspects of a linkage between these constituents in this linked entity. The atom identifier/name in the second of the two constituents containing the linkage. The chiral configuration of the second atom making the linkage. The component identifier in the second of the two constituents containing the linkage. The leaving atom identifier/name bonded to the second atom making the linkage. The value of attribute from_list_id in category pdbx_reference_linked_entity_link is a reference attribute list_id in category pdbx_reference_linked_entity_comp_list in the pdbx_reference_linked_entity_comp_list category. The atom identifier/name in the first of the two constituents containing the linkage. The component identifier in the first of the two constituents containing the linkage. The bond order target for the chemical linkage. The value of attribute link_id in category pdbx_reference_linked_entity_link uniquely identifies linkages within the linked entity. The value of attribute linked_entity_id in category pdbx_reference_linked_entity_link is a reference attribute linked_entity_id in category pdbx_reference_linked_entity_comp_list in the pdbx_reference_linked_entity_comp_list category. Data items in the PDBX_REFERENCE_MOLECULE category record reference information about small polymer molecules. Example: 1 Actinomycin <PDBx:pdbx_reference_moleculeCategory> <PDBx:pdbx_reference_molecule prd_id="PRD_000001"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C62 H86 N12 O16</PDBx:formula> <PDBx:formula_weight>1255.5</PDBx:formula_weight> <PDBx:name>Actinomycin D</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000002"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:name>Actinomycin C</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000003"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C63 H88 N12 O16</PDBx:formula> <PDBx:formula_weight>1269.5</PDBx:formula_weight> <PDBx:name>Actinomycin C2</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000004"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C64 H90 N12 O16</PDBx:formula> <PDBx:formula_weight>1283.5</PDBx:formula_weight> <PDBx:name>Actinomycin C3</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000005"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C62 H86 N12 O17</PDBx:formula> <PDBx:formula_weight>1271.5</PDBx:formula_weight> <PDBx:name>Actinomycin X0 beta</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000006"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C62 H85 F N12 O16</PDBx:formula> <PDBx:formula_weight>1273.49</PDBx:formula_weight> <PDBx:name>8-Fluoro-Actinomycin D</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000007"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C62 H84 N12 O17</PDBx:formula> <PDBx:formula_weight>1269.4</PDBx:formula_weight> <PDBx:name>Actinomycin X2</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000008"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C62 H84 N12 O19</PDBx:formula> <PDBx:formula_weight>1301.5</PDBx:formula_weight> <PDBx:name>Actinomycin Z1</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000009"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C62 H83 Cl N12 O18</PDBx:formula> <PDBx:formula_weight>1319.845</PDBx:formula_weight> <PDBx:name>Actinomycin Z3</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000010"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C62 H87 N13 O16</PDBx:formula> <PDBx:formula_weight>1270.43</PDBx:formula_weight> <PDBx:name>7-AminoActinomycin</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> <PDBx:pdbx_reference_molecule prd_id="PRD_000011"> <PDBx:class>polypeptide antibiotic</PDBx:class> <PDBx:formula>C61 H85 N13 O16</PDBx:formula> <PDBx:formula_weight>1256.4051</PDBx:formula_weight> <PDBx:name>N8-Actinomycin D</PDBx:name> <PDBx:type>Antitumor Antibiotic</PDBx:type> </PDBx:pdbx_reference_molecule> </PDBx:pdbx_reference_moleculeCategory> For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule. 0Z3 CD9 Broadly defines the function of the entity. Evidence for the assignment of attribute class in category pdbx_reference_molecule Special details about this molecule. Description of this molecule. The formula for the reference entity. Formulae are written according to the rules: 1. Only recognised element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each element symbol and its count, but in general parentheses are not used. 4. The order of elements depends on whether or not carbon is present. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S Formula mass in daltons of the entity. A name of the entity. thiostrepton Defines the current PDB release status for this molecule definition. Assigns the identifier of the reference molecule that has replaced this molecule. Assigns the identifier for the reference molecule which have been replaced by this reference molecule. Multiple molecule identifier codes should be separated by commas. Defines how this entity is represented in PDB data files. The PDB accession code for the entry containing a representative example of this molecule. Defines the structural classification of the entity. Peptide-like Macrolide Evidence for the assignment of attribute type in category pdbx_reference_molecule The value of attribute prd_id in category pdbx_reference_molecule is the unique identifier for the reference molecule in this family. By convention this ID uniquely identifies the reference molecule in in the PDB reference dictionary. The ID has the template form PRD_dddddd (e.g. PRD_000001) Data items in the PDBX_REFERENCE_MOLECULE_ANNOTATION category specify additional annotation relevant to the molecular entities. Example: 1 Actinomycin <PDBx:pdbx_reference_molecule_annotationCategory> <PDBx:pdbx_reference_molecule_annotation family_prd_id="FAM_000001" ordinal="1"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>KEGG</PDBx:source> <PDBx:text>RNA polymerase inhibitor</PDBx:text> <PDBx:type>Function</PDBx:type> </PDBx:pdbx_reference_molecule_annotation> <PDBx:pdbx_reference_molecule_annotation family_prd_id="FAM_000001" ordinal="2"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>KEGG</PDBx:source> <PDBx:text>antineoplastic</PDBx:text> <PDBx:type>Function</PDBx:type> </PDBx:pdbx_reference_molecule_annotation> <PDBx:pdbx_reference_molecule_annotation family_prd_id="FAM_000001" ordinal="3"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>DrugBank</PDBx:source> <PDBx:text>Nucleic Acid Synthesis Inhibitor</PDBx:text> <PDBx:type>Function</PDBx:type> </PDBx:pdbx_reference_molecule_annotation> <PDBx:pdbx_reference_molecule_annotation family_prd_id="FAM_000001" ordinal="4"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>DrugBank</PDBx:source> <PDBx:text>Protein Synthesis Inhibitor</PDBx:text> <PDBx:type>Function</PDBx:type> </PDBx:pdbx_reference_molecule_annotation> <PDBx:pdbx_reference_molecule_annotation family_prd_id="FAM_000001" ordinal="5"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>Norine</PDBx:source> <PDBx:text>antibiotic</PDBx:text> <PDBx:type>Function</PDBx:type> </PDBx:pdbx_reference_molecule_annotation> <PDBx:pdbx_reference_molecule_annotation family_prd_id="FAM_000001" ordinal="6"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>Norine</PDBx:source> <PDBx:text>antitumor</PDBx:text> <PDBx:type>Function</PDBx:type> </PDBx:pdbx_reference_molecule_annotation> <PDBx:pdbx_reference_molecule_annotation family_prd_id="FAM_000001" ordinal="7"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>PubChem</PDBx:source> <PDBx:text>transcriptional inhibitor</PDBx:text> <PDBx:type>Function</PDBx:type> </PDBx:pdbx_reference_molecule_annotation> </PDBx:pdbx_reference_molecule_annotationCategory> For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule. 0Z3 CD9 This data item is a pointer to attribute prd_id in category pdbx_reference_molecule in the PDB_REFERENCE_MOLECULE category. The source of the annoation for this entity. depositor provided from UniProt Entry P200311 Text describing the experimentation or computational evidence for the annotation. fluoresence measurements using flow cytometry kinase binding assay Text describing the annotation for this entity. antigen binding glucose transporter activity Type of annotation for this entity. Function Use Pharmacology Mechanism_of_Action Biological_Activity Inhibitor_Class Therapeutic_Category Research_Use Other_annotation The value of attribute family_prd_id in category pdbx_reference_molecule_annotation is a reference to attribute family_prd_id in category pdbx_reference_molecule_list in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST. This data item distinguishes anotations for this entity. Data items in the PDBX_REFERENCE_MOLECULE_DETAILS category records textual details about small polymer molecules. Example: 1 Actinomycin <PDBx:pdbx_reference_molecule_detailsCategory> <PDBx:pdbx_reference_molecule_details family_prd_id="FAM_000001" ordinal="1"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>Wikipedia</PDBx:source> <PDBx:text> Actinomycin D is primarily used as an investigative tool in cell biology to inhibit transcription. It does this by binding DNA at the transcription initiation complex and preventing elongation by RNA polymerase. Because it can bind DNA duplexes, it can also interfere with DNA replication, although other chemicals such as hydroxyurea are better suited for use in the laboratory as inhibitors of DNA synthesis.</PDBx:text> </PDBx:pdbx_reference_molecule_details> <PDBx:pdbx_reference_molecule_details family_prd_id="FAM_000001" ordinal="2"> <PDBx:prd_id>PRD_000001</PDBx:prd_id> <PDBx:source>DrugBank</PDBx:source> <PDBx:text> A compound composed of a two cyclic peptides attached to a phenoxazine that is derived from streptomyces parvullus. It binds to DNA and inhibits RNA synthesis (transcription), with chain elongation more sensitive than initiation, termination, or release. As a result of impaired mRNA production, protein synthesis also declines after dactinomycin therapy.</PDBx:text> </PDBx:pdbx_reference_molecule_details> <PDBx:pdbx_reference_molecule_details family_prd_id="FAM_000001" ordinal="3"> <PDBx:prd_id>PRD_000003</PDBx:prd_id> <PDBx:source>DOI</PDBx:source> <PDBx:source_id>DOI:10.1016/S0960-894X(98)00345-X</PDBx:source_id> <PDBx:text> Actinomycin D, C2 and VII, cyclic peptides, inhibit Grb2 SH2 domain association with a phosphotyrosine containing peptide derived from the Shc protein (pTyr317). Actinomycins are the first examples of nonphosphorylated natural ligands of SH2 domain.</PDBx:text> </PDBx:pdbx_reference_molecule_details> </PDBx:pdbx_reference_molecule_detailsCategory> The value of attribute prd_id in category pdbx_reference_molecule_details is a reference to attribute prd_id in category pdbx_reference_molecule in the PDBX_REFERENCE_MOLECULE category. A data source of this information (e.g. PubMed, Merck Index) A identifier within the data source for this information. The text of the description of special aspects of the entity. The value of attribute family_prd_id in category pdbx_reference_molecule_details is a reference to attribute family_prd_id' in category pdbx_reference_molecule_list in category PDBX_REFERENCE_MOLECULE_FAMILY. The value of attribute ordinal in category pdbx_reference_molecule_details is an ordinal that distinguishes each descriptive text for this entity. Data items in the PDBX_REFERENCE_MOLECULE_FAMILY category identify entity families. Example: 1 Actinomycin <PDBx:pdbx_reference_molecule_familyCategory> <PDBx:pdbx_reference_molecule_family family_prd_id="FAM_000001"> <PDBx:name>ACTINOMYCIN</PDBx:name> </PDBx:pdbx_reference_molecule_family> </PDBx:pdbx_reference_molecule_familyCategory> The entity family name. actinomycin adriamycin Assigns the current PDB release status for this family. Assigns the identifier of the family that has replaced this component. Assigns the identifier for the family which have been replaced by this family. Multiple family identifier codes should be separated by commas. The value of attribute family_prd_id in category pdbx_reference_entity must uniquely identify a record in the PDBX_REFERENCE_MOLECULE_FAMILY list. By convention this ID uniquely identifies the reference family in in the PDB reference dictionary. The ID has the template form FAM_dddddd (e.g. FAM_000001) Additional features associated with the reference entity. Example: 1 Actinomycin <PDBx:pdbx_reference_molecule_featuresCategory> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="1" prd_id="PRD_000001"> <PDBx:source>CAS</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>50-76-0</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="2" prd_id="PRD_000001"> <PDBx:source>Merck</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>14:2800</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="3" prd_id="PRD_000001"> <PDBx:source>Beilstein</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>4173766</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="4" prd_id="PRD_000001"> <PDBx:source>DrugBank</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>DB00970</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="5" prd_id="PRD_000001"> <PDBx:source>Norine</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>NOR00228</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="6" prd_id="PRD_000001"> <PDBx:source>PubChem</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>2019</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="7" prd_id="PRD_000001"> <PDBx:source>ChemSpider</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>1942</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="8" prd_id="PRD_000001"> <PDBx:source>ChEBI</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>27666</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="9" prd_id="PRD_000001"> <PDBx:source>ChemDB</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>3965267</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="10" prd_id="PRD_000001"> <PDBx:source>ChemIDplus</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>000050760</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="11" prd_id="PRD_000001"> <PDBx:source>ChemBank</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>External_Reference_ID</PDBx:type> <PDBx:value>329</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="12" prd_id="PRD_000001"> <PDBx:source>KEGG</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>KEGG_CompoundID</PDBx:type> <PDBx:value>C06770</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="13" prd_id="PRD_000001"> <PDBx:source>KEGG</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>KEGG_DrugID</PDBx:type> <PDBx:value>D00214</PDBx:value> </PDBx:pdbx_reference_molecule_features> <PDBx:pdbx_reference_molecule_features family_prd_id="FAM_000001" ordinal="14" prd_id="PRD_000001"> <PDBx:source>MESH</PDBx:source> <PDBx:source_ordinal>1</PDBx:source_ordinal> <PDBx:type>MESH_Unique_ID</PDBx:type> <PDBx:value>D003609</PDBx:value> </PDBx:pdbx_reference_molecule_features> </PDBx:pdbx_reference_molecule_featuresCategory> For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule. 0Z3 CD9 The information source for the component feature. PDB CHEBI DRUGBANK PUBCHEM The value of attribute source_ordinal in category pdbx_reference_molecule_features provides the priority order of features from a particular source or database. The entity feature type. FUNCTION ENZYME INHIBITED STRUCTURE IMAGE URL The entity feature value. The value of attribute family_prd_id in category pdbx_reference_molecule_features is a reference to attribute family_prd_id in category pdbx_reference_molecule_list in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST. The value of attribute ordinal in category pdbx_reference_molecule_features distinguishes each feature for this entity. The value of attribute prd_id in category pdbx_reference_molecule_features is a reference attribute prd_id in category pdbx_reference_molecule in the PDBX_REFERENCE_MOLECULE category. Data items in the PDBX_REFERENCE_MOLECULE_LIST category record reference information about small polymer molecules. Example: 1 Actinomycin <PDBx:pdbx_reference_molecule_listCategory> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000001"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000002"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000003"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000004"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000005"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000006"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000007"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000008"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000009"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000010"></PDBx:pdbx_reference_molecule_list> <PDBx:pdbx_reference_molecule_list family_prd_id="FAM_000001" prd_id="PRD_000011"></PDBx:pdbx_reference_molecule_list> </PDBx:pdbx_reference_molecule_listCategory> The value of attribute family_prd_id in category pdbx_reference_molecule_list is a reference to attribute family_prd_id' in category pdbx_reference_molecule_family in category PDBX_REFERENCE_MOLECULE_FAMILY. The value of attribute prd_id in category pdbx_reference_molecule_list is the unique identifier for the reference molecule in this family. By convention this ID uniquely identifies the reference molecule in in the PDB reference dictionary. The ID has the template form PRD_dddddd (e.g. PRD_000001) Data items in the PDBX_REFERENCE_MOLECULE_RELATED_STRUCTURES category record details of the structural examples in related databases for this entity. Example 1 - Actinomycin <PDBx:pdbx_reference_molecule_related_structuresCategory> <PDBx:pdbx_reference_molecule_related_structures family_prd_id="FAM_000001" ordinal="1"> <PDBx:citation_id>1</PDBx:citation_id> <PDBx:db_accession>144860</PDBx:db_accession> <PDBx:db_code>POHMUU</PDBx:db_code> <PDBx:db_name>CCDC</PDBx:db_name> <PDBx:formula>C72 H90 N12 O18</PDBx:formula> <PDBx:name>2,2&apos;-D-bis(O-Methyltyrosinyl)-actinomycin D ethyl acetate hydrate</PDBx:name> </PDBx:pdbx_reference_molecule_related_structures> <PDBx:pdbx_reference_molecule_related_structures family_prd_id="FAM_000001" ordinal="2"> <PDBx:citation_id>2</PDBx:citation_id> <PDBx:db_accession>140332</PDBx:db_accession> <PDBx:db_code>ZZZGQM</PDBx:db_code> <PDBx:db_name>CCDC</PDBx:db_name> <PDBx:name>Actinomycin</PDBx:name> </PDBx:pdbx_reference_molecule_related_structures> <PDBx:pdbx_reference_molecule_related_structures family_prd_id="FAM_000001" ordinal="3"> <PDBx:citation_id>2</PDBx:citation_id> <PDBx:db_accession>140333</PDBx:db_accession> <PDBx:db_code>ZZZGQM01</PDBx:db_code> <PDBx:db_name>CCDC</PDBx:db_name> <PDBx:name>Actinomycin</PDBx:name> </PDBx:pdbx_reference_molecule_related_structures> <PDBx:pdbx_reference_molecule_related_structures family_prd_id="FAM_000001" ordinal="4"> <PDBx:citation_id>3</PDBx:citation_id> <PDBx:db_accession>36676</PDBx:db_accession> <PDBx:db_code>BEJXET</PDBx:db_code> <PDBx:db_name>CCDC</PDBx:db_name> <PDBx:formula>C62 H86 N12 O16; 2(C19 H25 N8 O10 P1)</PDBx:formula> <PDBx:name>bis(Deoxyguanylyl-(3&apos;-5&apos;)-deoxycytidine) actinomycin D hydrate</PDBx:name> </PDBx:pdbx_reference_molecule_related_structures> <PDBx:pdbx_reference_molecule_related_structures family_prd_id="FAM_000001" ordinal="5"> <PDBx:citation_id>4</PDBx:citation_id> <PDBx:db_accession>77327</PDBx:db_accession> <PDBx:db_code>GIDNUC</PDBx:db_code> <PDBx:db_name>CCDC</PDBx:db_name> <PDBx:formula>C62 H86 N12 O16</PDBx:formula> <PDBx:name>Actinomycin D ethanol solvate hydrate</PDBx:name> </PDBx:pdbx_reference_molecule_related_structures> <PDBx:pdbx_reference_molecule_related_structures family_prd_id="FAM_000001" ordinal="6"> <PDBx:citation_id>5</PDBx:citation_id> <PDBx:db_accession>128630</PDBx:db_accession> <PDBx:db_code>ACTDGU01</PDBx:db_code> <PDBx:db_name>CCDC</PDBx:db_name> <PDBx:name>Actinomycin D bis(deoxyguanosine) dodecahydrate</PDBx:name> </PDBx:pdbx_reference_molecule_related_structures> <PDBx:pdbx_reference_molecule_related_structures family_prd_id="FAM_000001" ordinal="7"> <PDBx:citation_id>6</PDBx:citation_id> <PDBx:db_accession>455</PDBx:db_accession> <PDBx:db_code>ACTDGU10</PDBx:db_code> <PDBx:db_name>CCDC</PDBx:db_name> <PDBx:name>Actinomycin D bis(deoxyguanosine) dodecahydrate</PDBx:name> </PDBx:pdbx_reference_molecule_related_structures> <PDBx:pdbx_reference_molecule_related_structures family_prd_id="FAM_000001" ordinal="8"> <PDBx:citation_id>6</PDBx:citation_id> <PDBx:db_accession>3032</PDBx:db_accession> <PDBx:db_code>BRAXGU</PDBx:db_code> <PDBx:db_name>CCDC</PDBx:db_name> <PDBx:name>7-Bromoactinomycin D bis(deoxyguanosine) undecahydrate</PDBx:name> </PDBx:pdbx_reference_molecule_related_structures> </PDBx:pdbx_reference_molecule_related_structuresCategory> A link to related reference information in the citation category. The database accession code for the related structure reference. 143108 The database identifier code for the related structure reference. QEFHUE The database name for the related structure reference. CCDC The formula for the reference entity. Formulae are written according to the rules: 1. Only recognised element symbols may be used. 2. Each element symbol is followed by a 'count' number. A count of '1' may be omitted. 3. A space or parenthesis must separate each element symbol and its count, but in general parentheses are not used. 4. The order of elements depends on whether or not carbon is present. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts. C18 H19 N7 O8 S The chemical name for the structure entry in the related database actinomycn The value of attribute family_prd_id in category pdbx_reference_molecule_related_structures is a reference to attribute family_prd_id in category pdbx_reference_molecule_list in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST. The value of attribute ordinal in category pdbx_reference_molecule_related_structures distinguishes related structural data for each entity. Data items in the PDBX_REFERENCE_MOLECULE_SYNONYMS category records synonym names for reference entities. Example: 1 Actinomycin <PDBx:pdbx_reference_molecule_synonymsCategory> <PDBx:pdbx_reference_molecule_synonyms family_prd_id="FAM_000001" ordinal="1" prd_id="PRD_000001"> <PDBx:name>ACTINOMYCIN</PDBx:name> <PDBx:source>PDB</PDBx:source> </PDBx:pdbx_reference_molecule_synonyms> <PDBx:pdbx_reference_molecule_synonyms family_prd_id="FAM_000001" ordinal="2" prd_id="PRD_000001"> <PDBx:name> 3H-Phenoxazine-1,9-dicarboxamide, 2-amino-N,N&apos;-bis(hexadecahydro-6,13-diisopropyl-2,5,9-trimethyl-1,4,7,11,14-pentaoxo- 1H-pyrrolo[2,1-i][1,4,7,10,13]oxatetraazacyclohexadecin-10-yl)-4,6-dimethyl-3-oxo-(7CI)</PDBx:name> <PDBx:source>SciFinder</PDBx:source> </PDBx:pdbx_reference_molecule_synonyms> <PDBx:pdbx_reference_molecule_synonyms family_prd_id="FAM_000001" ordinal="3" prd_id="PRD_000001"> <PDBx:name>Actinomycin C1 (6CI)</PDBx:name> <PDBx:source>SciFinder</PDBx:source> </PDBx:pdbx_reference_molecule_synonyms> <PDBx:pdbx_reference_molecule_synonyms family_prd_id="FAM_000001" ordinal="4" prd_id="PRD_000001"> <PDBx:name>1H-Pyrrolo[2,1-i][1,4,7,10,13]oxatetraazacyclohexadecine, cyclic peptide deriv.</PDBx:name> <PDBx:source>SciFinder</PDBx:source> </PDBx:pdbx_reference_molecule_synonyms> <PDBx:pdbx_reference_molecule_synonyms family_prd_id="FAM_000001" ordinal="5" prd_id="PRD_000001"> <PDBx:name>3H-Phenoxazine, actinomycin D deriv.</PDBx:name> <PDBx:source>SciFinder</PDBx:source> </PDBx:pdbx_reference_molecule_synonyms> <PDBx:pdbx_reference_molecule_synonyms family_prd_id="FAM_000001" ordinal="6" prd_id="PRD_000001"> <PDBx:name>Actactinomycin A IV</PDBx:name> <PDBx:source>SciFinder</PDBx:source> </PDBx:pdbx_reference_molecule_synonyms> <PDBx:pdbx_reference_molecule_synonyms family_prd_id="FAM_000001" ordinal="7" prd_id="PRD_000001"> <PDBx:name>Actinomycin 7</PDBx:name> <PDBx:source>SciFinder</PDBx:source> </PDBx:pdbx_reference_molecule_synonyms> </PDBx:pdbx_reference_molecule_synonymsCategory> For entities represented as single molecules, the identifier corresponding to the chemical definition for the molecule. 0Z3 CD9 A synonym name for the entity. thiostrepton The source of this synonym name for the entity. CAS The value of attribute family_prd_id in category pdbx_reference_molecule_synonyms is a reference to attribute family_prd_id in category pdbx_reference_molecule_list in category PDBX_REFERENCE_MOLECULE_FAMILY_LIST. The value of attribute ordinal in category pdbx_reference_molecule_synonyms is an ordinal to distinguish synonyms for this entity. The value of attribute prd_id in category pdbx_reference_molecule_synonyms is a reference attribute prd_id in category pdbx_reference_molecule in the PDBX_REFERENCE_MOLECULE category. Data items in the PDBX_REFERENCE_PUBLICATION_LIST hold reference information related to PDB citation data. Example 1 - <PDBx:pdbx_reference_publication_listCategory> <PDBx:pdbx_reference_publication_list publication_abbrev="acc.CHEM.RES."> <PDBx:ASTM_code_type>ASTM</PDBx:ASTM_code_type> <PDBx:ASTM_code_value>ACHRE4</PDBx:ASTM_code_value> <PDBx:ISSN_code_type>ISSN</PDBx:ISSN_code_type> <PDBx:ISSN_code_value>0001-4842</PDBx:ISSN_code_value> <PDBx:country>US</PDBx:country> </PDBx:pdbx_reference_publication_list> </PDBx:pdbx_reference_publication_listCategory> The American Society for Testing and Materials (ASTM) code type. The American Society for Testing and Materials (ASTM) code assignment. The International Standard Serial Number (ISSN/ISBN/ESSN) code type. The International Standard Serial Number (ISSN) code value. The country/region of publication. Year in which publication terminated operation. Year in which publications began operation.. Abbreviated name of the reference publication. J. Mol. Biol. Data items in the PDBX_REFINE category record details about additional structure refinement parameters which are needed to complete legacy REMARK 3 refinement templates in PDB format files. Example 1 - PDB placeholders for refinement program SHELX <PDBx:pdbx_refineCategory> <PDBx:pdbx_refine entry_id="ABC001" pdbx_refine_id="x-ray"> <PDBx:R_factor_all_4sig_cutoff>0.174</PDBx:R_factor_all_4sig_cutoff> <PDBx:R_factor_obs_4sig_cutoff>0.169</PDBx:R_factor_obs_4sig_cutoff> <PDBx:free_R_factor_4sig_cutoff>0.216</PDBx:free_R_factor_4sig_cutoff> <PDBx:free_R_val_test_set_ct_4sig_cutoff>164</PDBx:free_R_val_test_set_ct_4sig_cutoff> <PDBx:free_R_val_test_set_size_perc_4sig_cutoff>1.29</PDBx:free_R_val_test_set_size_perc_4sig_cutoff> <PDBx:number_reflns_obs_4sig_cutoff>1263</PDBx:number_reflns_obs_4sig_cutoff> </PDBx:pdbx_refine> </PDBx:pdbx_refineCategory> R-value (all reflections, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 0.174 R-value (all reflections, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. R-value (working set, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 0.169 R-value (working set reflections, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. Free R-value error(no cutoff) R free value (4 sigma cutoff). Placeholder for PDB mapping of SHELXL refinement data. 0.216 Free R-value (no cutoff) Placeholder for PDB mapping of SHELXL refinement data. Free R-value (4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. Free R-value (no cutoff) Free R-value test set count (4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 164 Free R-value test set count (no cutoff) Placeholder for PDB mapping of SHELXL refinement data. Free R-value test set size (in percent, 4 sigma cutoff) Placeholder for PDB mapping of SHELXL refinement data. 1.29 Free R-value test set size (in percent, no cutoff) Placeholder for PDB mapping of SHELXL refinement data. Total number of reflections (4 sigma cutoff). Placeholder for PDB mapping of SHELXL refinement data. 1263 Total number of reflections (no cutoff). Placeholder for PDB mapping of SHELXL refinement data. This data item is a pointer to attribute id in category entry in the ENTRY category. This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category pdbx_refine can be used to distinguish the results of joint refinements. Auxilary parameter and topology files used in refinement. <PDBx:pdbx_refine_aux_fileCategory> <PDBx:pdbx_refine_aux_file pdbx_refine_id="x-ray" serial_no="1"> <PDBx:file_name>parm_hol.dat</PDBx:file_name> <PDBx:file_type>PARAMETER</PDBx:file_type> </PDBx:pdbx_refine_aux_file> </PDBx:pdbx_refine_aux_fileCategory> Auxilary file name. PARAM_NDBX_HIGH.DNA Auxilary file type. PARAMETER This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category pdbx_refine_aux_file can be used to distinguish the results of joint refinements. Serial number. Data items in the PDBX_REFINE_COMPONENT category record statistics of the final model relative to the density map. Example 1 - The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site The average isotropic B factors for the group of atoms (e.g. residue or ligand, side chain, main chain). The B factors for each atom is given by attribute B_iso_or_equiv in category atom_site A component of the identifier for the component. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site ATOM_SITE category. A component of the identifier for the component. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the component. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the component. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The index of connectivity is the product of the (2Fobs-Fcal) electron density values for the backbone atoms (N, CA and C) divided by the average value for the structure. Low values (less than 1.0) of this index indicate breaks in the backbone electron density which may be due to flexibility of the chain or incorrect tracing. connect = [(D(xi)...D(xi))^(1/N)] /<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 Correlation coefficient of electron density for each residue or ligand, side chain, main chain The density correlation coefficient is calculated for each component from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of atoms of the component (backbone or side chain). <Rcalc> is the mean of "calculated" densities of component atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 The index of density is the product of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 1.0) may be problematic for model fitting. index = [(D(xi)...D(xi))^(1/N)] /<D>_all Where : D(xi) = (2*Fobs - Fcal) <D>_all is the averaged value of density for the structure. The product is for N atoms of group. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group. The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group. The density ratio is similar to the density index, but summation of the density for the group is used for calculation. The ratio of density is the summation of the (2Fobs-Fcal) electron density values for the group of atoms divided by the average value for the structure. Low values (less than 0.4) of this ratio may be problematic for the group. index = [Sum~i D(xi)]/<D>_all Where: D(xi) = (2*Fobs - Fcal) <D>_all is the average value of density for the structure. The summation is for all the atoms of group. Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689 Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689 Real space R factor of electron density for each component, residue side chain, or main chain. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689 The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 The tendency of the group of atoms (e.g. residue or ligand, side chain, main chain) to move away from its current position. Displacement of atoms from electron density is estimated from the difference (Fobs - Fcal) map. The displacement vector is the ratio of the gradient of difference density to the curvature. The amplitude of the displacement vector is an indicator of the positional error. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 A component of the identifier for the component. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for the component. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the component. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the component. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Holds details of NCS restraints in cases where multiple conditions are provided for each domain. The number of this type of restraint applied to the domain specified by attribute dom_id in category pdbx_refine_ls_restr_ncs and in the domains against which it was restrained. 402 The root-mean-square deviation in restraints for the domain specified by attribute dom_id in category pdbx_refine_ls_restr_ncs and in the domains against which it was restrained. 0.49 The type of restraint applied to the domain specified by attribute dom_id in category pdbx_refine_ls_restr_ncs and in the domains against which it was restrained. 0.49 The value of the weighting coefficient used in non-crystalographic restaint in the domain specified by attribute dom_id in category pdbx_refine_ls_restr_ncs to equivalent atomic positions in the domains against which it was restrained. 0.50 This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. d1 Data items in the REFINE_TLS category record details about TLS parameters used in structure refinement. Note that the intention is primarily to describe directly refined TLS parameters, although other methods of obtaining TLS parameters may be covered, see item attribute method in category pdbx_refine_tls The [1][1] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[1][1] in category pdbx_refine_tls. The [1][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[1][2] in category pdbx_refine_tls. The [1][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[1][3] in category pdbx_refine_tls. The [2][2] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[2][2] in category pdbx_refine_tls. The [2][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[2][3] in category pdbx_refine_tls. The [3][3] element of the libration tensor L. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute L[3][3] in category pdbx_refine_tls. The [1][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. The estimated standard deviation of attribute S[1][1] in category pdbx_refine_tls. The [1][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[1][2] in category pdbx_refine_tls. The [1][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[1][3] in category pdbx_refine_tls. The [2][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[2][1] in category pdbx_refine_tls. The [2][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. The estimated standard deviation of attribute S[2][2] in category pdbx_refine_tls. The [2][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[2][3] in category pdbx_refine_tls. The [3][1] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[3][1] in category pdbx_refine_tls. The [3][2] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The estimated standard deviation of attribute S[3][2] in category pdbx_refine_tls. The [3][3] element of the screw-rotation tensor S. This should be given in the same coordinate frame as the corresponding anisotropic displacement parameters. The trace of S is indeterminate by crystallography, and should be set to zero. The estimated standard deviation of attribute S[3][3] in category pdbx_refine_tls. The [1][1] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[1][1] in category pdbx_refine_tls. The [1][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[1][2] in category pdbx_refine_tls. The [1][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[1][3] in category pdbx_refine_tls. The [2][2] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[2][2] in category pdbx_refine_tls. The [2][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[2][3] in category pdbx_refine_tls. The [3][3] element of the translation tensor T. This should be given in the same coordinate frame and units as the corresponding anisotropic displacement parameters. The estimated standard deviation of attribute T[3][3] in category pdbx_refine_tls. A description of the TLS group, such as a domain name or a chemical group name. Chain A catalytic domain Chain A Tyr 56 side chain The method by which the TLS parameters were obtained. The x coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The y coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric The z coordinate in angstroms of the origin to which the TLS parameters are referred, specified according to a set of orthogonal Cartesian axes related to the cell axes as given in attribute Cartn_transform_axes. in category atom_sites If the origin is omitted, it is assumed to be the centre of reaction of the group, in which case S must be symmetric This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category pdbx_refine_tls can be used to distinguish the results of joint refinements. The value of attribute id in category pdbx_refine_tls must uniquely identify a record in the PDBX_REFINE_TLS list. Note that this item need not be a number; it can be any unique identifier. 1 A Data items in the PDBX_REFINE_TLS_GROUP category record details about a fragment of a TLS group. Properties of the TLS group are recorded in PDBX_REFINE_TLS A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. O 2B3 A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. 1 5A A component of the identifier for the residue at which the TLS fragment range begins. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. O 2B3 A component of the identifier for the residue at which the TLS fragment range begins. 1 303 A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. O 2B3 A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. 1 5A A component of the identifier for the residue at which the TLS fragment range ends. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. O 2B3 A component of the identifier for the residue at which the TLS fragment range ends. 1 303 This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category pdbx_refine_tls_group can be used to distinguish the results of joint refinements. This data item is a pointer to attribute id in category pdbx_refine_tls in the REFINE_TLS category. A qualification of the subset of atoms in the specified range included in the TLS fragment. all atoms in specified range all main chain atoms only mnc side chain atoms only sdc A text description of subset of atoms included included in the TLS fragment. The value of attribute id in category pdbx_refine_tls_group must uniquely identify a record in the REFINE_TLS_GROUP list for a particular refinement. Note that this item need not be a number; it can be any unique identifier. 1 A The binning of the per-reflection signal generated by the software specified by attribute pdbx_signal_software_id. in category reflns If any reflections have a signal >= to the highest threshold specified, an additional bin should be inferred to hold them. Examples 1 - based on an internal STARANISO run <PDBx:pdbx_refln_signal_binningCategory> <PDBx:pdbx_refln_signal_binning ordinal="1"> <PDBx:upper_threshold>1.20</PDBx:upper_threshold> </PDBx:pdbx_refln_signal_binning> <PDBx:pdbx_refln_signal_binning ordinal="2"> <PDBx:upper_threshold>7.22</PDBx:upper_threshold> </PDBx:pdbx_refln_signal_binning> <PDBx:pdbx_refln_signal_binning ordinal="3"> <PDBx:upper_threshold>19.00</PDBx:upper_threshold> </PDBx:pdbx_refln_signal_binning> <PDBx:pdbx_refln_signal_binning ordinal="4"> <PDBx:upper_threshold>36.81</PDBx:upper_threshold> </PDBx:pdbx_refln_signal_binning> <PDBx:pdbx_refln_signal_binning ordinal="5"> <PDBx:upper_threshold>48.87</PDBx:upper_threshold> </PDBx:pdbx_refln_signal_binning> <PDBx:pdbx_refln_signal_binning ordinal="6"> <PDBx:upper_threshold>53.84</PDBx:upper_threshold> </PDBx:pdbx_refln_signal_binning> <PDBx:pdbx_refln_signal_binning ordinal="7"> <PDBx:upper_threshold>57.69</PDBx:upper_threshold> </PDBx:pdbx_refln_signal_binning> </PDBx:pdbx_refln_signal_binningCategory> The upper (exclusive) threshold of the bin. The ordinal number of the bin, ordered from lowest signal to highest. Details decribing crystallographic twinning. Example 1 - <PDBx:pdbx_reflns_twinCategory> <PDBx:pdbx_reflns_twin crystal_id="1" diffrn_id="1" operator="h,-h-k,-l"> <PDBx:fraction>.43</PDBx:fraction> <PDBx:mean_F_square_over_mean_F2>.84</PDBx:mean_F_square_over_mean_F2> <PDBx:mean_I2_over_mean_I_square>1.3</PDBx:mean_I2_over_mean_I_square> <PDBx:type>merohedral</PDBx:type> </PDBx:pdbx_reflns_twin> </PDBx:pdbx_reflns_twinCategory> An identifier for the twin domain. The twin fraction or twin factor represents a quantitative parameter for the crystal twinning. The value 0 represents no twinning, < 0.5 partial twinning, = 0.5 for perfect twinning. The ideal statistics for twinned crystals. The values calculated with the acentric data are given below. Statistic Untwinned data Perfect twinned data <I^2>/<I>^2 2.0 1.5 <F>^2/<F^2> 0.785 0.865 References: Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and Overcoming Crystal Twinning. and information from the following on-line sites: CNS site http://cns.csb.yale.edu/v1.1/ CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html The ideal statistics for twinned crystals. The values calculated with the acentric data are given below. Statistic Untwinned data Perfect twinned data <I^2>/<I>^2 2.0 1.5 <F>^2/<F^2> 0.785 0.865 References: Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and Overcoming Crystal Twinning. and information from the following on-line sites: CNS site http://cns.csb.yale.edu/v1.1/ CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html There are two types of twinning: merohedral or hemihedral non-merohedral or epitaxial For merohedral twinning the diffraction patterns from the different domains are completely superimposable. Hemihedral twinning is a special case of merohedral twinning. It only involves two distinct domains. Pseudo-merohedral twinning is a subclass merohedral twinning in which lattice is coincidentally superimposable. In the case of non-merohedral or epitaxial twinning the reciprocal lattices do not superimpose exactly. In this case the diffraction pattern consists of two (or more) interpenetrating lattices, which can in principle be separated. The crystal identifier. A reference to attribute id in category exptl_crystal in category EXPTL_CRYSTAL. The diffraction data set identifier. A reference to attribute id in category diffrn in category DIFFRN. The possible merohedral or hemihedral twinning operators for different point groups are: True point group Twin operation hkl related to 3 2 along a,b h,-h-k,-l 2 along a*,b* h+k,-k,-l 2 along c -h,-k,l 4 2 along a,b,a*,b* h,-k,-l 6 2 along a,b,a*,b* h,-h-k,-l 321 2 along a*,b*,c -h,-k,l 312 2 along a,b,c -h,-k,l 23 4 along a,b,c k,-h,l References: Yeates, T.O. (1997) Methods in Enzymology 276, 344-358. Detecting and Overcoming Crystal Twinning. and information from the following on-line sites: CNS site http://cns.csb.yale.edu/v1.1/ CCP4 site http://www.ccp4.ac.uk/dist/html/detwin.html SHELX site http://shelx.uni-ac.gwdg.de/~rherbst/twin.html h,-h-k,-l h+k,-k,-l -h,-k,l h,-k,-l k,-h,l Data items in the PDBX_RELATED_DATA_SET category record references to experimental data sets related to the entry. Example 1 - <PDBx:pdbx_related_exp_data_setCategory> <PDBx:pdbx_related_exp_data_set ordinal="1"> <PDBx:data_reference>10.000/10002/image_data/cif</PDBx:data_reference> <PDBx:data_set_type>diffraction image data</PDBx:data_set_type> <PDBx:details>imgCIF data set containing 500 frames</PDBx:details> <PDBx:metadata_reference>10.000/10002/image_data/txt</PDBx:metadata_reference> </PDBx:pdbx_related_exp_data_set> </PDBx:pdbx_related_exp_data_setCategory> A DOI reference to the related data set. 10.000/10002/image_data/cif The type of the experimenatal data set. diffraction image data NMR free induction decay data Additional details describing the content of the related data set and its application to the current investigation. A DOI reference to the metadata decribing the related data set. 10.000/10002/image_data/txt Ordinal identifier for each related experimental data set. Data items in the PDBX_REMEDIATION_ATOM_SITE_MAPPING category records mapping information between selected molecular entities that have been chemically redefined. The prior and current atom nomenclature is tabulated in this category. Example component QUA <PDBx:pdbx_remediation_atom_site_mappingCategory> <PDBx:pdbx_remediation_atom_site_mapping id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:auth_alt_id xsi:nil="true" /> <PDBx:auth_asym_id>C</PDBx:auth_asym_id> <PDBx:auth_atom_id>O12</PDBx:auth_atom_id> <PDBx:auth_comp_id>QUA</PDBx:auth_comp_id> <PDBx:auth_seq_id>7</PDBx:auth_seq_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>O12</PDBx:label_atom_id> <PDBx:label_comp_id>QUA</PDBx:label_comp_id> <PDBx:label_seq_id>0</PDBx:label_seq_id> <PDBx:pdbx_align>1</PDBx:pdbx_align> <PDBx:pre_PDB_ins_code xsi:nil="true" /> <PDBx:pre_auth_alt_id xsi:nil="true" /> <PDBx:pre_auth_asym_id>C</PDBx:pre_auth_asym_id> <PDBx:pre_auth_atom_id>O12</PDBx:pre_auth_atom_id> <PDBx:pre_auth_comp_id>QUA</PDBx:pre_auth_comp_id> <PDBx:pre_auth_seq_id>7</PDBx:pre_auth_seq_id> <PDBx:pre_group_PDB>HETATM</PDBx:pre_group_PDB> <PDBx:pre_pdbx_align>1</PDBx:pre_pdbx_align> </PDBx:pdbx_remediation_atom_site_mapping> <PDBx:pdbx_remediation_atom_site_mapping id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:auth_alt_id xsi:nil="true" /> <PDBx:auth_asym_id>C</PDBx:auth_asym_id> <PDBx:auth_atom_id>C11</PDBx:auth_atom_id> <PDBx:auth_comp_id>QUA</PDBx:auth_comp_id> <PDBx:auth_seq_id>7</PDBx:auth_seq_id> <PDBx:group_PDB>HETATM</PDBx:group_PDB> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>C</PDBx:label_asym_id> <PDBx:label_atom_id>C11</PDBx:label_atom_id> <PDBx:label_comp_id>QUA</PDBx:label_comp_id> <PDBx:label_seq_id>0</PDBx:label_seq_id> <PDBx:pdbx_align>1</PDBx:pdbx_align> <PDBx:pre_PDB_ins_code xsi:nil="true" /> <PDBx:pre_auth_alt_id xsi:nil="true" /> <PDBx:pre_auth_asym_id>C</PDBx:pre_auth_asym_id> <PDBx:pre_auth_atom_id>C11</PDBx:pre_auth_atom_id> <PDBx:pre_auth_comp_id>QUA</PDBx:pre_auth_comp_id> <PDBx:pre_auth_seq_id>7</PDBx:pre_auth_seq_id> <PDBx:pre_group_PDB>HETATM</PDBx:pre_group_PDB> <PDBx:pre_pdbx_align>1</PDBx:pre_pdbx_align> </PDBx:pdbx_remediation_atom_site_mapping> </PDBx:pdbx_remediation_atom_site_mappingCategory> Optional atom_site identifier. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the current atom_site identifier labeling alternate locations. A component of the current atom_site identifier. This data item corresponds to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the current atom_site identifier. This data item corrresponds to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the current atom_site identifier. This data item corresponds to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the current atom_site identifier. This data item corresponds to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The PDB group of atoms to which the atom site belongs. A component of the atom_site identifier. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The fraction of the atom type present at the current atom site. An optional alignment flag. A component of the prior atom_site identifier. This data item corresponds to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item corresponds to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item corrresponds to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item corresponds to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item corresponds to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This item corresponds to the PDB group of atoms to which the atom site belongs. The fraction of the atom type present for the prior atom site. An optional alignment flag. The value of pdbx_remediation_atom_site_mapping.id must uniquely identify a record in the PDBX_REMEDIATION_ATOM_SITE_MAPPING list. Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_RMCH_OUTLIER category list the residues with torsion angles outside the expected Ramachandran regions. This is a completely derived category. Do not edit. Identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number for the given residue The phi value that for the residue that lies outside normal regions of the Rammachandran plot The Psi value that for the residue that lies outside of the normal region of the rammachandran plot The value of attribute id in category pdbx_rmch_outlier must uniquely identify each item in the PDBX_RMCH_OUTLIER list. This is an integer serial number. Data items in the PDBX_RMS_DEVS_COV_BY_MONOMER record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards. Example 1 - <PDBx:pdbx_rms_devs_cov_by_monomerCategory> <PDBx:pdbx_rms_devs_cov_by_monomer id="1"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_seq_id>1</PDBx:auth_seq_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>A</PDBx:label_comp_id> <PDBx:label_seq_id>1</PDBx:label_seq_id> <PDBx:model_id xsi:nil="true" /> <PDBx:num_bonds>12</PDBx:num_bonds> <PDBx:rms_bonds>0.05</PDBx:rms_bonds> </PDBx:pdbx_rms_devs_cov_by_monomer> </PDBx:pdbx_rms_devs_cov_by_monomerCategory> This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number Total number of angles in calculation of attribute rms_angles in category pdbx_rms_devs_cov_by_monomer. Total number of bonds in calculation of attribute rms_bonds in category pdbx_rms_devs_cov_by_monomer. RMS deviation for all angles in this monomer relative to small molecule crystal standards. RMS deviation for all bonds in this monomer relative to small molecule crystal standards. The value of attribute id in category pdbx_rms_devs_cov_by_monomer must uniquely identify each item in the PDBX_RMS_DEVS_COV_BY_MONOMER list. This is an integer serial number. Data items in the PDBX_RMS_DEVS_COVALENT record the summary RMS deviations for nucleic acid covalent geometry relative to small molecule crystal standards. Example 1 - <PDBx:pdbx_rms_devs_covalentCategory> <PDBx:pdbx_rms_devs_covalent entry_id="1ABC"> <PDBx:num_bonds>100</PDBx:num_bonds> <PDBx:rms_bonds>0.89</PDBx:rms_bonds> </PDBx:pdbx_rms_devs_covalent> </PDBx:pdbx_rms_devs_covalentCategory> Total number of angles in calculation of attribute rms_angles in category pdbx_rms_devs_covalent. Total number of base angles in calculation of attribute rms_angles_base in category pdbx_rms_devs_covalent. Total number of sugar angles in calculation of attribute rms_angles_phosphate in category pdbx_rms_devs_covalent. Total number of sugar angles in calculation of attribute rms_angles_sugar in category pdbx_rms_devs_covalent. Total number of bonds in calculation of attribute rms_bonds in category pdbx_rms_devs_covalent. Total number of base bonds in calculation of attribute rms_bonds_base in category pdbx_rms_devs_covalent. Total number of sugar bonds in calculation of attribute rms_bonds_phosphate in category pdbx_rms_devs_covalent. Total number of sugar bonds in calculation of attribute rms_bonds_sugar in category pdbx_rms_devs_covalent. Total RMS deviation for all angles in entry relative to small molecule crystal standards. Total RMS deviation for all base angles in entry relative to small molecule crystal standards. Total RMS deviation for all phosphate angles in entry relative to small molecule crystal standards. Total RMS deviation for all sugar angles in entry relative to small molecule crystal standards. Total RMS deviation for all bonds in entry relative to small molecule crystal standards. Total RMS deviation for all base bonds in entry relative to small molecule crystal standards. Total RMS deviation for all phosphate bonds in entry relative to small molecule crystal standards. Total RMS deviation for all sugar bonds in entry relative to small molecule crystal standards. Pointer to the entry id. The details about each robotic system used to collect data for this project. The name of the manufacturer of the robotic system. The model of the robotic system. The type of robotic system used for in the production pathway. Assign a numerical ID to each instrument. Data items in the PDBX_SEQ_MAP_DEPOSITOR_INFO record the details about the mapping sample and coordinate sequences. Example 1 - <PDBx:pdbx_seq_map_depositor_infoCategory> <PDBx:pdbx_seq_map_depositor_info auth_asym_id="A" entity_id="1"> <PDBx:one_letter_code>AAAAAAAAAAAAAAAAA</PDBx:one_letter_code> <PDBx:one_letter_code_mod>AAAAAAAAAAAAAAAAA</PDBx:one_letter_code_mod> </PDBx:pdbx_seq_map_depositor_info> </PDBx:pdbx_seq_map_depositor_infoCategory> Coordinate sequence expressed as string of one-letter residue codes. Coordinate sequence expressed as string of one-letter residue codes with nonstandard residues expressed as 3-letter codes in parentheses. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute entity_id in category entity_poly in the ENTITY_POLY category. PDBX_SEQUENCE_ANNOTATION holds internal details about molecular sequences described in the context of PDB chains. <PDBx:pdbx_sequence_annotationCategory> <PDBx:pdbx_sequence_annotation pdb_chain_id="A"> <PDBx:ncbi_taxid>188000</PDBx:ncbi_taxid> </PDBx:pdbx_sequence_annotation> </PDBx:pdbx_sequence_annotationCategory> NCBI TaxID PDB chain ID. Data items in the PDBX_SEQUENCE_PATTERN category record the number of occurences of common step sequence patterns (e.g. AA, CG, AT). Example 1 - <PDBx:pdbx_sequence_patternCategory> <PDBx:pdbx_sequence_pattern label_asym_id="A" sequence_pattern="GC"> <PDBx:pattern_count>2</PDBx:pattern_count> </PDBx:pdbx_sequence_pattern> <PDBx:pdbx_sequence_pattern label_asym_id="B" sequence_pattern="GC"> <PDBx:pattern_count>2</PDBx:pattern_count> </PDBx:pdbx_sequence_pattern> </PDBx:pdbx_sequence_patternCategory> The identifier of the author asym_id of the strand containing the sequence pattern. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Number of occurences of the sequence pattern within the named strand. The identifier of the asym_id of the strand containing the sequence pattern. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Sequence singlet or doublet. Data items in the PDBX_SEQUENCE_RANGE category identify the beginning and ending points of polypeptide sequence segments. Example 1 - <PDBx:pdbx_sequence_rangeCategory> <PDBx:pdbx_sequence_range beg_label_alt_id="A" beg_label_asym_id="A" beg_label_comp_id="PRO" beg_label_seq_id="1" end_label_alt_id="A" end_label_asym_id="A" end_label_comp_id="GLY" end_label_seq_id="29" seq_range_id="s1"></PDBx:pdbx_sequence_range> <PDBx:pdbx_sequence_range beg_label_alt_id="A" beg_label_asym_id="D" beg_label_comp_id="PRO" beg_label_seq_id="91" end_label_alt_id="A" end_label_asym_id="D" end_label_comp_id="GLY" end_label_seq_id="119" seq_range_id="s2"></PDBx:pdbx_sequence_range> </PDBx:pdbx_sequence_rangeCategory> A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the sequence range ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This data item is an identifier for a sequence range. Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_DATA_REDUCTION category record details about data processing that are unique to XFEL experiments. These will compliment data recorded in category pdbx_diffrn_merge_stat. Example 1 <PDBx:pdbx_serial_crystallography_data_reductionCategory> <PDBx:pdbx_serial_crystallography_data_reduction diffrn_id="1"> <PDBx:crystal_hits>1797503</PDBx:crystal_hits> <PDBx:frames_indexed>578620</PDBx:frames_indexed> <PDBx:frames_total>7324430</PDBx:frames_total> </PDBx:pdbx_serial_crystallography_data_reduction> </PDBx:pdbx_serial_crystallography_data_reductionCategory> For experiments in which samples are provided in a continuous stream, the total number of frames collected in which the crystal was hit. 1200 5750 For experiments in which samples are provided in a continuous stream, the total number of frames collected in which a droplet was hit. 1200 5750 For experiments in which samples are provided in a continuous stream, the total number of data frames collected in which the sample was hit. 1200 5750 For experiments in which samples are provided in a continuous stream, the total number of data frames collected that contained a "hit" but failed to index. 1200 5750 For experiments in which samples are provided in a continuous stream, the total number of data frames collected that were indexed. 1200 5750 The total number of data frames collected for this data set. 20 100 For experiments in which samples are provided in a continuous stream, the total number of lattices indexed. 1200 5750 For FEL experiments, the number of pulse events in the dataset. For FEL experiments, in which data collection was performed in batches, indicates which subset of the data collected were used in producing this dataset. The data item is a pointer to attribute id in category diffrn in the DIFFRN category. 1 Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_MEASUREMENT category record details the beam that is impinging on the sample Example 1 <PDBx:pdbx_serial_crystallography_measurementCategory> <PDBx:pdbx_serial_crystallography_measurement diffrn_id="1"> <PDBx:collection_time_total>16.95</PDBx:collection_time_total> <PDBx:focal_spot_size>1.8</PDBx:focal_spot_size> <PDBx:photons_per_pulse>0.17</PDBx:photons_per_pulse> <PDBx:pulse_duration>45</PDBx:pulse_duration> </PDBx:pdbx_serial_crystallography_measurement> </PDBx:pdbx_serial_crystallography_measurementCategory> The total number of hours required to measure this data set. 120.0 The collimation or type of focusing optics applied to the radiation. Kirkpatrick-Baez mirrors Beryllium compound refractive lenses Fresnel zone plates The focal spot size of the beam impinging on the sample (micrometres squared). The photons per pulse measured in (tera photons (10^(12)^)/pulse units). The average duration (femtoseconds) of the pulse energy measured at the sample. The energy/pulse of the X-ray pulse impacting the sample measured in microjoules. The photon energy of the X-ray pulse measured in KeV. The distance from source to the sample along the optical axis (metres). The dimension of the source beam measured at the source (micrometres squared). For FEL experiments, the pulse repetition rate measured in cycles per seconds. The data item is a pointer to attribute id in category diffrn in the DIFFRN category. 1 Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY category record general details about the sample delivery Example 1 <PDBx:pdbx_serial_crystallography_sample_deliveryCategory> <PDBx:pdbx_serial_crystallography_sample_delivery diffrn_id="1"> <PDBx:description>LCP injector</PDBx:description> </PDBx:pdbx_serial_crystallography_sample_delivery> </PDBx:pdbx_serial_crystallography_sample_deliveryCategory> The description of the mechanism by which the specimen in placed in the path of the source. fixed target electrospin MESH CoMESH gas dynamic virtual nozzle LCP injector addressable microarray The description of the mechanism by which the specimen in placed in the path of the source. The data item is a pointer to attribute id in category diffrn in the DIFFRN category. 1 Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY_FIXED_TARGET category record details about sample delivery using a fixed taget. Example 1 <PDBx:pdbx_serial_crystallography_sample_delivery_fixed_targetCategory> <PDBx:pdbx_serial_crystallography_sample_delivery_fixed_target diffrn_id="1"> <PDBx:crystals_per_unit>7</PDBx:crystals_per_unit> <PDBx:sample_holding>mesh</PDBx:sample_holding> <PDBx:support_base>goniometer</PDBx:support_base> </PDBx:pdbx_serial_crystallography_sample_delivery_fixed_target> </PDBx:pdbx_serial_crystallography_sample_delivery_fixed_targetCategory> The number of crystals per dropplet or pore in fixed target For a fixed target sample, a description of sample preparation Any details pertinent to the fixed sample target Device used to control movement of the fixed sample DMC-4080 Method to prevent dehydration of sample seal humidifed gas flash freezing For a fixed target sample, mechanism to hold sample in the beam mesh loop grid The sample solution content and concentration Size of pore in grid supporting sample. Diameter or length in micrometres, e.g. pore diameter Type of base holding the support goniometer Velocity of sample horizontally relative to a perpendicular beam in millimetres/second Velocity of sample vertically relative to a perpendicular beam in millimetres/second The data item is a pointer to attribute id in category diffrn in the DIFFRN category. 1 Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY_INJECTION category record details about sample delivery by injection Example 1 <PDBx:pdbx_serial_crystallography_sample_delivery_injectionCategory> <PDBx:pdbx_serial_crystallography_sample_delivery_injection diffrn_id="1"> <PDBx:carrier_solvent>liquid</PDBx:carrier_solvent> <PDBx:description>microextrusion injector</PDBx:description> <PDBx:flow_rate>0.22</PDBx:flow_rate> <PDBx:injector_diameter>50</PDBx:injector_diameter> </PDBx:pdbx_serial_crystallography_sample_delivery_injection> </PDBx:pdbx_serial_crystallography_sample_delivery_injectionCategory> For continuous sample flow experiments, the carrier buffer used to move the sample into the beam. Should include protein concentration. LCP grease liquid For continuous sample flow experiments, the concentration of crystals in the solution being injected. The concentration is measured in million crystals/ml. For continuous sample flow experiments, a description of the injector used to move the sample into the beam. microextrusion injector The size of filter in micrometres in filtering crystals For continuous sample flow experiments, the flow rate of solution being injected measured in ul/min. For continuous sample flow experiments, the diameter of the injector in micrometres. The type of nozzle to deliver and focus sample jet gas GDVN For continuous sample flow experiments, the mean pressure in kilopascals at which the sample is injected into the beam. For continuous sample flow experiments, the temperature in Kelvins of the speciman injected. This may be different from the temperature of the sample. Diameter in micrometres of jet stream of sample delivery Sample deliver driving force, e.g. Gas, Electronic Potential syringe gas electronic potential Details of crystal growth and preparation of the crystals Crystals transfered to carrier solvent at room temperature The data item is a pointer to attribute id in category diffrn in the DIFFRN category. 1 Data items in the PDBX_SOLN_SCATTER category record details about a solution scattering experiment Example 1 - based on PDB entry 1HAQ <PDBx:pdbx_soln_scatterCategory> <PDBx:pdbx_soln_scatter entry_id="1HAQ" id="1"> <PDBx:buffer_name>tris</PDBx:buffer_name> <PDBx:concentration_range>0.7 - 14</PDBx:concentration_range> <PDBx:detector_specific xsi:nil="true" /> <PDBx:detector_type>500-channel quadrant</PDBx:detector_type> <PDBx:max_mean_cross_sectional_radii_gyration>1.7</PDBx:max_mean_cross_sectional_radii_gyration> <PDBx:max_mean_cross_sectional_radii_gyration_esd>0.1</PDBx:max_mean_cross_sectional_radii_gyration_esd> <PDBx:mean_guiner_radius>11.1</PDBx:mean_guiner_radius> <PDBx:mean_guiner_radius_esd>0.4</PDBx:mean_guiner_radius_esd> <PDBx:min_mean_cross_sectional_radii_gyration>4.4</PDBx:min_mean_cross_sectional_radii_gyration> <PDBx:min_mean_cross_sectional_radii_gyration_esd>0.2</PDBx:min_mean_cross_sectional_radii_gyration_esd> <PDBx:num_time_frames>10</PDBx:num_time_frames> <PDBx:protein_length>40</PDBx:protein_length> <PDBx:sample_pH xsi:nil="true" /> <PDBx:source_beamline>2.1</PDBx:source_beamline> <PDBx:source_beamline_instrument xsi:nil="true" /> <PDBx:source_class>synchrotron</PDBx:source_class> <PDBx:source_type>SRS BEAMLINE 2.1</PDBx:source_type> <PDBx:temperature>288</PDBx:temperature> <PDBx:type>x-ray</PDBx:type> </PDBx:pdbx_soln_scatter> <PDBx:pdbx_soln_scatter entry_id="1HAQ" id="2"> <PDBx:buffer_name>PBS in 99.9&#37; D2O</PDBx:buffer_name> <PDBx:concentration_range>0.4 - 9.6</PDBx:concentration_range> <PDBx:detector_specific xsi:nil="true" /> <PDBx:detector_type>area</PDBx:detector_type> <PDBx:max_mean_cross_sectional_radii_gyration>1.51</PDBx:max_mean_cross_sectional_radii_gyration> <PDBx:max_mean_cross_sectional_radii_gyration_esd>0.06</PDBx:max_mean_cross_sectional_radii_gyration_esd> <PDBx:mean_guiner_radius>11.3</PDBx:mean_guiner_radius> <PDBx:mean_guiner_radius_esd>0.4</PDBx:mean_guiner_radius_esd> <PDBx:min_mean_cross_sectional_radii_gyration>3.9</PDBx:min_mean_cross_sectional_radii_gyration> <PDBx:min_mean_cross_sectional_radii_gyration_esd>0.2</PDBx:min_mean_cross_sectional_radii_gyration_esd> <PDBx:num_time_frames xsi:nil="true" /> <PDBx:protein_length>37.0 - 39.0</PDBx:protein_length> <PDBx:sample_pH xsi:nil="true" /> <PDBx:source_beamline xsi:nil="true" /> <PDBx:source_beamline_instrument>D11, D22</PDBx:source_beamline_instrument> <PDBx:source_class>neutron source</PDBx:source_class> <PDBx:source_type>ILL</PDBx:source_type> <PDBx:temperature xsi:nil="true" /> <PDBx:type>neutron</PDBx:type> </PDBx:pdbx_soln_scatter> <PDBx:pdbx_soln_scatter entry_id="1HAQ" id="3"> <PDBx:buffer_name>PBS in 99.9&#37; D2O</PDBx:buffer_name> <PDBx:concentration_range>3.7, 6.1</PDBx:concentration_range> <PDBx:detector_specific xsi:nil="true" /> <PDBx:detector_type>AREA (TIME-OF-FLIGHT)</PDBx:detector_type> <PDBx:max_mean_cross_sectional_radii_gyration xsi:nil="true" /> <PDBx:max_mean_cross_sectional_radii_gyration_esd xsi:nil="true" /> <PDBx:mean_guiner_radius>11.7</PDBx:mean_guiner_radius> <PDBx:mean_guiner_radius_esd>0.5</PDBx:mean_guiner_radius_esd> <PDBx:min_mean_cross_sectional_radii_gyration xsi:nil="true" /> <PDBx:min_mean_cross_sectional_radii_gyration_esd xsi:nil="true" /> <PDBx:num_time_frames xsi:nil="true" /> <PDBx:protein_length>40.0</PDBx:protein_length> <PDBx:sample_pH xsi:nil="true" /> <PDBx:source_beamline>Pulsed Neutron</PDBx:source_beamline> <PDBx:source_beamline_instrument>LOQ</PDBx:source_beamline_instrument> <PDBx:source_class>neutron source</PDBx:source_class> <PDBx:source_type>ISIS</PDBx:source_type> <PDBx:temperature xsi:nil="true" /> <PDBx:type>neutron</PDBx:type> </PDBx:pdbx_soln_scatter> </PDBx:pdbx_soln_scatterCategory> The name of the buffer used for the sample in the solution scattering experiment. acetic acid The concentration range (mg/mL) of the complex in the sample used in the solution scattering experiment to determine the mean radius of structural elongation. 0.7 - 14 A list of the software used in the data analysis SCTPL5 GNOM A list of the software used in the data reduction OTOKO The particular radiation detector. In general this will be a manufacturer, description, model number or some combination of these. The general class of the radiation detector. The maximum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q gives the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The estimated standard deviation for the mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The estimated standard deviation for the minimum mean radius of structural elongation of the sample. In a given solute-solvent contrast, the radius of gyration R_G is a measure of structural elongation if the internal inhomogeneity of scattering densities has no effect. Guiner analysis at low Q give the R_G and the forward scattering at zero angle I(0). lnl(Q) = lnl(0) - R_G^2Q^2/3 where Q = 4(pi)sin(theta/lamda) 2theta = scattering angle lamda = wavelength The above expression is valid in a QR_G range for extended rod-like particles. The relative I(0)/c values ( where c = sample concentration) for sample measurements in a constant buffer for a single sample data session, gives the relative masses of the protein(s) studied when referenced against a standard. see: O.Glatter & O.Kratky, (1982). Editors of "Small angle X-ray Scattering, Academic Press, New York. O.Kratky. (1963). X-ray small angle scattering with substances of biological interest in diluted solutions. Prog. Biophys. Chem., 13, 105-173. G.D.Wignall & F.S.Bates, (1987). The small-angle approximation of X-ray and neutron scatter from rigid rods of non-uniform cross section and finite length. J.Appl. Crystallog., 18, 452-460. If the structure is elongated, the mean radius of gyration of the cross-sectional structure R_XS and the mean cross sectional intensity at zero angle [I(Q).Q]_Q->0 is obtained from ln[I(Q).Q] = ln[l(Q).(Q)]_Q->0 - ((R_XS)^2Q^2)/2 The number of time frame solution scattering images used. The length (or range) of the protein sample under study. If the solution structure is approximated as an elongated elliptical cyclinder the length L is determined from, L = sqrt [12( (R_G)^2 - (R_XS)^2 ) ] The length should also be given by L = pi I(0) / [ I(Q).Q]_Q->0 The pH value of the buffered sample. The beamline name used for the experiment The instrumentation used on the beamline The general class of the radiation source. neutron source synchrotron The make, model, name or beamline of the source of radiation. The temperature in kelvins at which the experiment was conducted The type of solution scattering experiment carried out This data item is a pointer to attribute id in category entry in the ENTRY category. The value of attribute id in category pdbx_soln_scatter must uniquely identify the sample in the category PDBX_SOLN_SCATTER Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the homology model fitting to the solution scatter data. A description of the conformer selection criteria used. The modelled scattering curves were assessed by calculation of the RG, RSX-1 and RXS-2 values in the same Q ranges used in the experimental Guinier fits. models were then ranked using a goodness-of-fit R-factor defined by analogy with protein crystallography and based on the experimental curves in the Q range extending to 1.4 nm-1. A description of any additional details concerning the experiment. Homology models were built for the 17 SCR domains and energy minimisations were performed to improve the connectivity in the fh model. triantennary complex-type carbohydrate structures (MAN3GLCNAC6GAL3FUC3NEUNAC1) were added to each of the N-linked glycosylation sites. a library of linker peptide conformations was used in domain modelling constrained by the solution scattering fits. modelling with the scattering data was also carried out by rotational search methods. the x-ray and neutron scattering curve I(Q) was calculated assuming a uniform scattering density for the spheres using the debye equation as adapted to spheres. x-ray curves were calculated from the hydrated sphere models without corrections for wavelength spread or beam divergence, while these corrections were applied for the neutron curves but now using unhydrated models. A list of the entries used to fit the model to the scattering data PDB CODE 1HFI, 1HCC, 1HFH, 1VCC A description of the methods used in the modelling Constrained scattering fitting of homology models The number of model conformers calculated. The number of model conformers submitted in the entry The index of the representative conformer among the submitted conformers for the entry A list of the software authors MSI A list of the software used in the modeeling INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI The value of attribute id in category pdbx_soln_scatter_model must uniquely identify the sample in the category PDBX_SOLN_SCATTER_MODEL This data item is a pointer to attribute id in category pdbx_soln_scatter in the PDBX_SOLN_SCATTER category. Data items in the PDBX_SOLVENT_ATOM_SITE_MAPPING category records mapping information between solvent atoms before and after symmetry repositioning. Example - <PDBx:pdbx_solvent_atom_site_mappingCategory> <PDBx:pdbx_solvent_atom_site_mapping id="1"> <PDBx:Cartn_x xsi:nil="true" /> <PDBx:Cartn_y xsi:nil="true" /> <PDBx:Cartn_z xsi:nil="true" /> <PDBx:auth_alt_id xsi:nil="true" /> <PDBx:auth_asym_id xsi:nil="true" /> <PDBx:auth_atom_id xsi:nil="true" /> <PDBx:auth_comp_id xsi:nil="true" /> <PDBx:auth_seq_id xsi:nil="true" /> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id xsi:nil="true" /> <PDBx:label_atom_id xsi:nil="true" /> <PDBx:label_comp_id xsi:nil="true" /> <PDBx:label_seq_id xsi:nil="true" /> <PDBx:pre_Cartn_x xsi:nil="true" /> <PDBx:pre_Cartn_y xsi:nil="true" /> <PDBx:pre_Cartn_z xsi:nil="true" /> <PDBx:pre_auth_alt_id xsi:nil="true" /> <PDBx:pre_auth_asym_id xsi:nil="true" /> <PDBx:pre_auth_atom_id xsi:nil="true" /> <PDBx:pre_auth_comp_id xsi:nil="true" /> <PDBx:pre_auth_seq_id xsi:nil="true" /> </PDBx:pdbx_solvent_atom_site_mapping> </PDBx:pdbx_solvent_atom_site_mappingCategory> The x atom-site coordinate of the solvent position in angstroms. The y atom-site coordinate of the solvent position in angstroms. The z atom-site coordinate of the solvent position in angstroms. Optional atom_site identifier. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the current atom_site identifier labeling alternate locations. A component of the current atom_site identifier. This data item corresponds to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the current atom_site identifier. This data item corrresponds to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the current atom_site identifier. This data item corresponds to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the current atom_site identifier. This data item corresponds to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the atom_site identifier. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The fraction of the atom type present at the current atom site. The prior x atom-site coordinate of the solvent position in angstroms. The prior y atom-site coordinate of the solvent position in angstroms. The prior z atom-site coordinate of the solvent position in angstroms. A component of the prior atom_site identifier. This data item corresponds to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item corresponds to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item corrresponds to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item corresponds to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the prior atom_site identifier. This data item corresponds to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the target solvent atom 7th symm. posn.; +a on x; -b on y 7_645 The symmetry applied to the target solvent atom. The symmetry equivalent position is given in the 'xyz' representation. The value of pdbx_solvent_atom_site_mapping.id must uniquely identify a record in the PDBX_SOLVENT_ATOM_SITE_MAPPING list. Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_SOLVENT_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated. Example 1 - based on NDB entry DDH048 <PDBx:pdbx_solvent_infoCategory> <PDBx:pdbx_solvent_info id="1"> <PDBx:name>water</PDBx:name> <PDBx:numb_per_asym_unit>22</PDBx:numb_per_asym_unit> </PDBx:pdbx_solvent_info> </PDBx:pdbx_solvent_infoCategory> Name of solvent. WATER Number of solvent molecules per asymmetric unit. 22 Serial number. 1 Data item will still be used until the ENTITY category is fully adopted by NDBQuery. Example 1 - based on NDB entry BDL001 <PDBx:pdbx_sourceCategory> <PDBx:pdbx_source src_method="synthetic"></PDBx:pdbx_source> </PDBx:pdbx_sourceCategory> Source of biological unit. Mostly: SYNTHETIC synthetic Data items in the PDBX_STEREOCHEMISTRY identify chiral centers and associated chiral volumes. Out-of-plane angle for neighbor W This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. Alt_id for stereochemically related atom U. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. Alt_id for stereochemically related atom V. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. Alt_id for stereochemically related atom W. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. Stereochemically related atom U. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. Stereochemically related atom V. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. Stereochemically related atom W. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number for the given angle Chiral volume in degrees. (U x V) * W The value of attribute id in category pdbx_stereochemistry must uniquely identify each item in the PDBX_STEREOCHEMISTRY list. This is an integer serial number. Data items in the PDBX_STRUCT_ASSEMBLY category record details about the structural elements that form macromolecular assemblies. Example 1 - <PDBx:pdbx_struct_assemblyCategory> <PDBx:pdbx_struct_assembly id="1"> <PDBx:details> The icosahedral virus particle.</PDBx:details> </PDBx:pdbx_struct_assembly> </PDBx:pdbx_struct_assemblyCategory> A description of special aspects of the macromolecular assembly. The icosahedral virus particle. Provides details of the method used to determine or compute the assembly. The number of polymer molecules in the assembly. Provides the details of the oligomeric state of the assembly. monomer octameric tetradecameric eicosameric 21-meric 60-meric 180-meric helical The value of attribute id in category pdbx_struct_assembly must uniquely identify a record in the PDBX_STRUCT_ASSEMBLY list. Provides reason a particular assembly in pdbx_struct_assembly is of interest. Example 1 - <PDBx:pdbx_struct_assembly_auth_classificationCategory> <PDBx:pdbx_struct_assembly_auth_classification assembly_id="1"> <PDBx:reason_for_interest>biologically relevant</PDBx:reason_for_interest> </PDBx:pdbx_struct_assembly_auth_classification> <PDBx:pdbx_struct_assembly_auth_classification assembly_id="2"> <PDBx:reason_for_interest>designed</PDBx:reason_for_interest> </PDBx:pdbx_struct_assembly_auth_classification> </PDBx:pdbx_struct_assembly_auth_classificationCategory> Provides the reason that a particular assembly is being studied This item references an assembly in pdbx_struct_assembly Provides author supplied evidentiary support for assemblies in pdbx_struct_assembly. Example 1 - <PDBx:pdbx_struct_assembly_auth_evidenceCategory> <PDBx:pdbx_struct_assembly_auth_evidence assembly_id="1" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:experimental_support>cross-linking</PDBx:experimental_support> </PDBx:pdbx_struct_assembly_auth_evidence> <PDBx:pdbx_struct_assembly_auth_evidence assembly_id="1" id="2"> <PDBx:details>Elutes as a dimer</PDBx:details> <PDBx:experimental_support>gel filtration</PDBx:experimental_support> </PDBx:pdbx_struct_assembly_auth_evidence> <PDBx:pdbx_struct_assembly_auth_evidence assembly_id="2" id="3"> <PDBx:details xsi:nil="true" /> <PDBx:experimental_support>cross-linking</PDBx:experimental_support> </PDBx:pdbx_struct_assembly_auth_evidence> </PDBx:pdbx_struct_assembly_auth_evidenceCategory> Provides any additional information regarding the evidence of this assembly Provides the experimental method to determine the state of this assembly This item references an assembly in pdbx_struct_assembly Identifies a unique record in pdbx_struct_assembly_auth_evidence. Provides author supplied evidentiary support for assemblies in pdbx_struct_assembly. Example 1 - <PDBx:pdbx_struct_assembly_auth_evidence_depositor_infoCategory> <PDBx:pdbx_struct_assembly_auth_evidence_depositor_info assembly_id="1" id="1"> <PDBx:details xsi:nil="true" /> <PDBx:experimental_support>cross-linking</PDBx:experimental_support> </PDBx:pdbx_struct_assembly_auth_evidence_depositor_info> <PDBx:pdbx_struct_assembly_auth_evidence_depositor_info assembly_id="1" id="2"> <PDBx:details>Elutes as a dimer</PDBx:details> <PDBx:experimental_support>gel filtration</PDBx:experimental_support> </PDBx:pdbx_struct_assembly_auth_evidence_depositor_info> <PDBx:pdbx_struct_assembly_auth_evidence_depositor_info assembly_id="2" id="3"> <PDBx:details xsi:nil="true" /> <PDBx:experimental_support>cross-linking</PDBx:experimental_support> </PDBx:pdbx_struct_assembly_auth_evidence_depositor_info> </PDBx:pdbx_struct_assembly_auth_evidence_depositor_infoCategory> Provides any additional information regarding the evidence of this assembly Provides the experimental method to determine the state of this assembly This item references an assembly in pdbx_struct_assembly Identifies a unique record in pdbx_struct_assembly_auth_evidence_depositor_info. Data items in the PDBX_STRUCT_ASSEMBLY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY. Example 1 - <PDBx:pdbx_struct_assembly_depositor_infoCategory> <PDBx:pdbx_struct_assembly_depositor_info id="1"> <PDBx:details> The icosahedral virus particle.</PDBx:details> </PDBx:pdbx_struct_assembly_depositor_info> </PDBx:pdbx_struct_assembly_depositor_infoCategory> A description of special aspects of the macromolecular assembly. The icosahedral virus particle. A flag to indicate that the depositor has provided matrix records Provides details of the method used to determine or compute the assembly. The number of polymer molecules in the assembly. Provides the details of the oligomeric state of the assembly. monomer octameric tetradecameric eicosameric 21-meric 60-meric 180-meric helical The name of a file containing matrix records. The value of attribute id in category pdbx_struct_assembly_depositor_info must uniquely identify a record in the PDBX_STRUCT_ASSEMBLY_DEPOSITOR_INFO list. Data items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about the generation of each macromolecular assemblies. The PDBX_STRUCT_ASSEMBLY_GEN data items provide the specifications of the components that constitute that assembly in terms of cartesian transformations. Example 1 - <PDBx:pdbx_struct_assembly_genCategory> <PDBx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="A" oper_expression="1"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="B" oper_expression="1"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="A" oper_expression="2"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="B" oper_expression="2"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="C" oper_expression="2"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="A" oper_expression="3"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="B" oper_expression="3"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="D" oper_expression="3"></PDBx:pdbx_struct_assembly_gen> </PDBx:pdbx_struct_assembly_genCategory> Example 2 - <PDBx:pdbx_struct_assembly_genCategory> <PDBx:pdbx_struct_assembly_gen assembly_id="1" asym_id_list="A,B" oper_expression="1"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="2" asym_id_list="A,B,C" oper_expression="2"></PDBx:pdbx_struct_assembly_gen> <PDBx:pdbx_struct_assembly_gen assembly_id="3" asym_id_list="A,B,D" oper_expression="3"></PDBx:pdbx_struct_assembly_gen> </PDBx:pdbx_struct_assembly_genCategory> This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. This item may be expressed as a comma separated list of identifiers. This data item is a pointer to attribute id in category pdbx_struct_entity_inst in the PDBX_STRUCT_ENTITY_INST category. This item may be expressed as a comma separated list of instance identifiers. This data item is a pointer to attribute id in category pdbx_struct_assembly in the PDBX_STRUCT_ASSEMBLY category. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. This item may be expressed as a comma separated list of identifiers. Identifies the operation of collection of operations from category PDBX_STRUCT_OPER_LIST. Operation expressions may have the forms: (1) the single operation 1 (1,2,5) the operations 1, 2, 5 (1-4) the operations 1,2,3 and 4 (1,2)(3,4) the combinations of operations 3 and 4 followed by 1 and 2 (i.e. the cartesian product of parenthetical groups applied from right to left) (1) (1,2,5) (1-60) (1-60)(61) Data items in the PDBX_STRUCT_ASSEMBLY_GEN_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_GEN. Example 1 - <PDBx:pdbx_struct_assembly_gen_depositor_infoCategory> <PDBx:pdbx_struct_assembly_gen_depositor_info id="1"> <PDBx:assembly_id>1</PDBx:assembly_id> <PDBx:asym_id_list>A</PDBx:asym_id_list> <PDBx:oper_expression>1</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="2"> <PDBx:assembly_id>1</PDBx:assembly_id> <PDBx:asym_id_list>B</PDBx:asym_id_list> <PDBx:oper_expression>1</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="3"> <PDBx:assembly_id>2</PDBx:assembly_id> <PDBx:asym_id_list>A</PDBx:asym_id_list> <PDBx:oper_expression>2</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="4"> <PDBx:assembly_id>2</PDBx:assembly_id> <PDBx:asym_id_list>B</PDBx:asym_id_list> <PDBx:oper_expression>2</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="5"> <PDBx:assembly_id>2</PDBx:assembly_id> <PDBx:asym_id_list>C</PDBx:asym_id_list> <PDBx:oper_expression>2</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="6"> <PDBx:assembly_id>3</PDBx:assembly_id> <PDBx:asym_id_list>A</PDBx:asym_id_list> <PDBx:oper_expression>3</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="7"> <PDBx:assembly_id>3</PDBx:assembly_id> <PDBx:asym_id_list>B</PDBx:asym_id_list> <PDBx:oper_expression>3</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="8"> <PDBx:assembly_id>3</PDBx:assembly_id> <PDBx:asym_id_list>D</PDBx:asym_id_list> <PDBx:oper_expression>3</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> </PDBx:pdbx_struct_assembly_gen_depositor_infoCategory> Example 2 - <PDBx:pdbx_struct_assembly_gen_depositor_infoCategory> <PDBx:pdbx_struct_assembly_gen_depositor_info id="1"> <PDBx:assembly_id>1</PDBx:assembly_id> <PDBx:asym_id_list>A,B</PDBx:asym_id_list> <PDBx:oper_expression>1</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="2"> <PDBx:assembly_id>2</PDBx:assembly_id> <PDBx:asym_id_list>A,B,C</PDBx:asym_id_list> <PDBx:oper_expression>2</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> <PDBx:pdbx_struct_assembly_gen_depositor_info id="3"> <PDBx:assembly_id>3</PDBx:assembly_id> <PDBx:asym_id_list>A,B,D</PDBx:asym_id_list> <PDBx:oper_expression>3</PDBx:oper_expression> </PDBx:pdbx_struct_assembly_gen_depositor_info> </PDBx:pdbx_struct_assembly_gen_depositor_infoCategory> Flag indicating that all polymer chains are used in the assembly Y This data item is a pointer to attribute id in category pdbx_struct_assembly in the PDBX_STRUCT_ASSEMBLY category. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. This item may be expressed as a comma separated list of identifiers. Flag indicating unit matrix Y This data item is the author provided chain names for the assembly This item may be expressed as a comma separated list of identifiers. A,B,C D,E,F,G,H Transformation matrix as provided by depositor 1 0 0 0 0 1 0 0 0 0 1 0 The axial rise per subunit in the helical assembly. 17.400000 Angular rotation (degrees) along the helical axis -34.616000 Identifies the operation of collection of operations from category PDBX_STRUCT_OPER_LIST. Operation expressions may have the forms: (1) the single operation 1 (1,2,5) the operations 1, 2, 5 (1-4) the operations 1,2,3 and 4 (1,2)(3,4) the combinations of operations 3 and 4 followed by 1 and 2 (i.e. the cartesian product of parenthetical groups applied from right to left) (1) (1,2,5) (1-60) (1-60)(61) This item expresses the transformation on an X, Y and Z basis. 1/2+x, 1/2-y, -z The value of attribute id in category pdbx_struct_assembly_gen_depositor_info must uniquely identify a record in the PDBX_STRUCT_ASSEMBLY_GEN_DEPOSITOR_INFO list. Properties and features of structural assemblies. Example 1 - <PDBx:pdbx_struct_assembly_propCategory> <PDBx:pdbx_struct_assembly_prop biol_id="1" type="ABSA"> <PDBx:details> </PDBx:details> <PDBx:value>1456.7</PDBx:value> </PDBx:pdbx_struct_assembly_prop> </PDBx:pdbx_struct_assembly_propCategory> Additional details about this assembly property. The value of the assembly property. The identifier for the assembly used in category PDBX_STRUCT_ASSEMBLY. The property type for the assembly. Data items in the PDBX_STRUCT_ASSEMBLY_PROP_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_PROP. Example 1 - <PDBx:pdbx_struct_assembly_prop_depositor_infoCategory> <PDBx:pdbx_struct_assembly_prop_depositor_info biol_id="1" type="ABSA"> <PDBx:value>1456.7</PDBx:value> </PDBx:pdbx_struct_assembly_prop_depositor_info> </PDBx:pdbx_struct_assembly_prop_depositor_infoCategory> Additional details about this assembly property. The value of the assembly property. The identifier for the assembly used in category STRUCT_BIOL. The property type for the assembly. Data items in the PDBX_STRUCT_ASYM_GEN category record details about the generation of the crystallographic asymmetric unit. The PDBX_STRUCT_ASYM_GEN data items provide the specifications of the components that constitute the asymmetric unit in terms of cartesian transformations of deposited coordinates. Example 1 - <PDBx:pdbx_struct_asym_genCategory> <PDBx:pdbx_struct_asym_gen entity_inst_id="A" oper_expression="1"> <PDBx:asym_id>A</PDBx:asym_id> </PDBx:pdbx_struct_asym_gen> <PDBx:pdbx_struct_asym_gen entity_inst_id="B" oper_expression="1"> <PDBx:asym_id>B</PDBx:asym_id> </PDBx:pdbx_struct_asym_gen> </PDBx:pdbx_struct_asym_genCategory> This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. This data item is a pointer to attribute id in category pdbx_struct_entity_inst in the PDBX_STRUCT_ENTITY_INST category. Identifies the operation from category PDBX_STRUCT_OPER_LIST. (1) (1-2) Data items in the PDBX_STRUCT_BIOL_FUNC category record details about the function of a particular biological assembly. Example 1 - based on NDB entry NRT0001 <PDBx:pdbx_struct_biol_funcCategory> <PDBx:pdbx_struct_biol_func biol_id="1" id="1"> <PDBx:function>Oxygen Transport</PDBx:function> </PDBx:pdbx_struct_biol_func> </PDBx:pdbx_struct_biol_funcCategory> The function assigned to the biological assembly. OXYGEN TRANSPORT This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL category. A code which must uniquely identify each function assigned to a biological assembly. Data items in the PDBX_STRUCT_CHEM_COMP_DIAGNOSTICS category provides structural diagnostics in chemical components instances. Example 1 - <PDBx:pdbx_struct_chem_comp_diagnosticsCategory> <PDBx:pdbx_struct_chem_comp_diagnostics ordinal="1"> <PDBx:asym_id>Q</PDBx:asym_id> <PDBx:auth_comp_id>Q20</PDBx:auth_comp_id> <PDBx:auth_seq_id>10</PDBx:auth_seq_id> <PDBx:details>Strained geometry. Long carbonyl bond at C10.</PDBx:details> <PDBx:pdb_strand_id>Q</PDBx:pdb_strand_id> <PDBx:seq_num xsi:nil="true" /> <PDBx:type>GEOMETRY</PDBx:type> </PDBx:pdbx_struct_chem_comp_diagnostics> </PDBx:pdbx_struct_chem_comp_diagnosticsCategory> Instance identifier for the polymer molecule. A B PDB component ID NAG ATP PDB position in the sequence. 1 2 Special structural details about this chemical component. Insertion code of the monomer or ligand . A B PDB strand/chain id. A B Position in the sequence. 1 2 A classification of the diagnostic for the chemical component instance An ordinal index for this category 1 2 Data items in the PDBX_STRUCT_CHEM_COMP_FEATURE category provides structural annotations in chemical components instances. Example 1 - <PDBx:pdbx_struct_chem_comp_featureCategory> <PDBx:pdbx_struct_chem_comp_feature ordinal="1"> <PDBx:asym_id>Q</PDBx:asym_id> <PDBx:auth_comp_id>Q20</PDBx:auth_comp_id> <PDBx:auth_seq_id>10</PDBx:auth_seq_id> <PDBx:details>Helix of length 4 beginning at atom position C2A.</PDBx:details> <PDBx:pdb_strand_id>Q</PDBx:pdb_strand_id> <PDBx:seq_num xsi:nil="true" /> <PDBx:type>SECONDARY STRUCTURE</PDBx:type> </PDBx:pdbx_struct_chem_comp_feature> </PDBx:pdbx_struct_chem_comp_featureCategory> Instance identifier for the polymer molecule. A B PDB component ID NAG ATP PDB position in the sequence. 1 2 Special structural details about this chemical component. Insertion code of the monomer or ligand . A B PDB strand/chain id. A B Position in the sequence. 1 2 A classification of the annotation for the chemical component instance An ordinal index for this category 1 2 Data items in the PDBX_STRUCT_CONN_ANGLE category record the angles in connections between portions of the structure. Example 1 PDB entry 2v8d <PDBx:pdbx_struct_conn_angleCategory> <PDBx:pdbx_struct_conn_angle id="1"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>114</PDBx:ptnr3_label_seq_id> <PDBx:value>104.7</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="2"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id> <PDBx:value>91.3</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="3"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id> <PDBx:value>120.6</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="4"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>2041</PDBx:ptnr3_label_seq_id> <PDBx:value>172.5</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="5"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>2041</PDBx:ptnr3_label_seq_id> <PDBx:value>80.0</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="6"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>226</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>2041</PDBx:ptnr3_label_seq_id> <PDBx:value>91.3</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="7"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id> <PDBx:value>76.9</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="8"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id> <PDBx:value>112.3</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="9"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>226</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id> <PDBx:value>127.0</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="10"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>2041</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id> <PDBx:value>95.9</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="11"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>OE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>GLU</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>160</PDBx:ptnr3_label_seq_id> <PDBx:value>89.8</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="12"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id> <PDBx:value>95.5</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="13"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>GLU</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>160</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>O</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HOH</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>3001</PDBx:ptnr3_label_seq_id> <PDBx:value>109.4</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="14"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>421</PDBx:ptnr3_label_seq_id> <PDBx:value>90.4</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="15"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>GLU</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>160</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>421</PDBx:ptnr3_label_seq_id> <PDBx:value>111.3</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="16"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>3001</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>A</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>421</PDBx:ptnr3_label_seq_id> <PDBx:value>138.9</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="17"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>3001</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>114</PDBx:ptnr3_label_seq_id> <PDBx:value>106.4</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="18"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>3001</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>OD</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>ASP</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>125</PDBx:ptnr3_label_seq_id> <PDBx:value>100.5</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="19"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>OD</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>ASP</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>125</PDBx:ptnr3_label_seq_id> <PDBx:value>115.6</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="20"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>O</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HOH</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>3001</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id> <PDBx:value>123.2</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="21"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>NE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>HIS</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>114</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id> <PDBx:value>123.2</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="22"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OD</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ASP</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>125</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>500</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>NE</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>HIS</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>226</PDBx:ptnr3_label_seq_id> <PDBx:value>82.7</PDBx:value> </PDBx:pdbx_struct_conn_angle> <PDBx:pdbx_struct_conn_angle id="23"> <PDBx:ptnr1_PDB_ins_code xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>OE</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>GLU</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>160</PDBx:ptnr1_label_seq_id> <PDBx:ptnr2_PDB_ins_code>ZN</PDBx:ptnr2_PDB_ins_code> <PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id xsi:nil="true" /> <PDBx:ptnr2_label_comp_id>ZN</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>501</PDBx:ptnr2_label_seq_id> <PDBx:ptnr3_PDB_ins_code>OD</PDBx:ptnr3_PDB_ins_code> <PDBx:ptnr3_label_asym_id>B</PDBx:ptnr3_label_asym_id> <PDBx:ptnr3_label_atom_id xsi:nil="true" /> <PDBx:ptnr3_label_comp_id>ASP</PDBx:ptnr3_label_comp_id> <PDBx:ptnr3_label_seq_id>125</PDBx:ptnr3_label_seq_id> <PDBx:value>148.6</PDBx:value> </PDBx:pdbx_struct_conn_angle> </PDBx:pdbx_struct_conn_angleCategory> A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the atom specified by attribute ptnr1_label* in category pdbx_struct_conn_angle to generate the first partner in the structure angle. 7th symm. posn.; +a on x; -b on y 7_645 A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_alt.id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the atom specified by attribute ptnr2_label* in category pdbx_struct_conn_angle to generate the second partner in the structure angle. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the structure angle. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure angle. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the atom specified by attribute ptnr3_label* in category pdbx_struct_conn_angle to generate the first partner in the structure angle. 7th symm. posn.; +a on x; -b on y 7_645 Angle in degrees defined by the three sites attribute ptnr1_label_atom_id, in category pdbx_struct_conn_angle attribute ptnr2_label_atom_id in category pdbx_struct_conn_angle attribute ptnr3_label_atom_id in category pdbx_struct_conn_angle The standard uncertainty (estimated standard deviation) of attribute value in category pdbx_struct_conn_angle The value of attribute id in category pdbx_struct_conn_angle must uniquely identify a record in the PDBX_STRUCT_CONN_ANGLE list. Note that this item need not be a number; it can be any unique identifier. Data items in the PDBX_STRUCT_ENTITY_INST category record details about the structural elements in the deposited entry. The entity instance is a method neutral identifier for the observed molecular entities in the deposited coordinate set. Example 1 - <PDBx:pdbx_struct_entity_instCategory> <PDBx:pdbx_struct_entity_inst id="A"> <PDBx:details>one monomer of the dimeric enzyme</PDBx:details> <PDBx:entity_id>1</PDBx:entity_id> </PDBx:pdbx_struct_entity_inst> <PDBx:pdbx_struct_entity_inst id="B"> <PDBx:details>one monomer of the dimeric enzyme</PDBx:details> <PDBx:entity_id>1</PDBx:entity_id> </PDBx:pdbx_struct_entity_inst> </PDBx:pdbx_struct_entity_instCategory> A description of special aspects of this portion of the contents of the deposited unit. The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. This data item is a pointer to attribute id in category entity in the ENTITY category. The value of attribute id in category pdbx_struct_entity_inst must uniquely identify a record in the PDBX_STRUCT_ENTITY_INST list. The entity instance is a method neutral identifier for the observed molecular entities in the deposited coordinate set. 1 A 2B3 Data items in the PDBX_STRUCT_GROUP_COMPONENT_RANGE category define a structural group as a continuous span chemical components. Example 1 - <PDBx:pdbx_struct_group_component_rangeCategory> <PDBx:pdbx_struct_group_component_range ordinal="1"> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:beg_PDB_ins_code xsi:nil="true" /> <PDBx:beg_auth_asym_id>A</PDBx:beg_auth_asym_id> <PDBx:beg_auth_comp_id>MLU</PDBx:beg_auth_comp_id> <PDBx:beg_auth_seq_id>1</PDBx:beg_auth_seq_id> <PDBx:end_PDB_ins_code xsi:nil="true" /> <PDBx:end_auth_asym_id>A</PDBx:end_auth_asym_id> <PDBx:end_auth_comp_id>RAM</PDBx:end_auth_comp_id> <PDBx:end_auth_seq_id>10</PDBx:end_auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_component_range> </PDBx:pdbx_struct_group_component_rangeCategory> Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component range in this group assignment. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute struct_group_id in category pdbx_struct_group_list in the PDBX_STRUCT_GROUP_LIST category. The value of attribute id in category pdbx_struct_group_component_range must uniquely identify a record in the PDBX_STRUCT_GROUP_COMPONENT_RANGE list. Data items in the PDBX_STRUCT_GROUP_COMPONENTS category list component-level group assignments within the entry. Groups are defined and described in category PDBX_STRUCT_GROUP_LIST. Example 1 <PDBx:pdbx_struct_group_componentsCategory> <PDBx:pdbx_struct_group_components ordinal="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>MLU</PDBx:auth_comp_id> <PDBx:auth_seq_id>1</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>OMZ</PDBx:auth_comp_id> <PDBx:auth_seq_id>2</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="3"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>ASN</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="4"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>GHP</PDBx:auth_comp_id> <PDBx:auth_seq_id>4</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="5"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>GHP</PDBx:auth_comp_id> <PDBx:auth_seq_id>5</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="6"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>OMX</PDBx:auth_comp_id> <PDBx:auth_seq_id>6</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="7"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>3FG</PDBx:auth_comp_id> <PDBx:auth_seq_id>7</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="8"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>ERE</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="9"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>BGC</PDBx:auth_comp_id> <PDBx:auth_seq_id>9</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> <PDBx:pdbx_struct_group_components ordinal="10"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>RAM</PDBx:auth_comp_id> <PDBx:auth_seq_id>10</PDBx:auth_seq_id> <PDBx:struct_group_id>1</PDBx:struct_group_id> </PDBx:pdbx_struct_group_components> </PDBx:pdbx_struct_group_componentsCategory> Part of the identifier for the component in this group assignment. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Part of the identifier for the component in this group assignment. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier for the component in this group assignment. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component in this group assignment. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component in this group assignment. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component in this group assignment. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component in this group assignment. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component in this group assignment. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the component in this group assignment. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The value of attribute group_id in category pdbx_struct_group_components identifies the group assignment for the component. This is a reference to the identifier for group definition in category PDBX_STRUCT_GROUP_LIST. The value of attribute ordinal in category pdbx_struct_group_components must uniquely identify each item in the PDBX_STRUCT_GROUP_COMPONENTS list. This is an integer serial number. Data items in the PDBX_STRUCT_GROUP_LIST define groups of related components or atoms. Example 1 - <PDBx:pdbx_struct_group_listCategory> <PDBx:pdbx_struct_group_list struct_group_id="1"> <PDBx:description> Decaplanin is a tricyclic glycopeptide. The scaffold is a heptapeptide with the configuration D-D-L-D-D-L-L, glycosylated by a monosaccharide and a disaccharide</PDBx:description> <PDBx:group_enumeration_type>component</PDBx:group_enumeration_type> <PDBx:name>DECAPLANIN</PDBx:name> <PDBx:type>MolecularComplex</PDBx:type> </PDBx:pdbx_struct_group_list> </PDBx:pdbx_struct_group_listCategory> The description of the group. The manner in which the group is defined. Groups consist of collections within the set of deposited coordinates which can be defined in terms of a list of chemical components in category PDBX_STRUCT_GROUP_COMPONENTS, ranges of chemical components in PDBX_STRUCT_GROUP_COMPONENT_RANGE, or as individual atoms using attribute pdbx_group_id. in category atom_site Groups can be composed of selections from multiple categories in which case the enumeration types are separated by commas. a list of components component a selection of listed components and component range selections component,component_range The name of the group. A qualification of the subset of atoms in the group. all atoms in specified range all main chain atoms only mnc side chain atoms only sdc A text description of subset of the atom selection in the group. A selected list of group types. The unique identifier for the group. Special features of this structural entry. Example 1 - <PDBx:pdbx_struct_infoCategory> <PDBx:pdbx_struct_info type="nonpolymer_zero_occupancy_flag" value="Y"></PDBx:pdbx_struct_info> <PDBx:pdbx_struct_info type="polymer_zero_occupancy_flag" value="Y"></PDBx:pdbx_struct_info> <PDBx:pdbx_struct_info type="multiple_model_flag" value="Y"></PDBx:pdbx_struct_info> <PDBx:pdbx_struct_info type="multiple_model_details" value="Model 3 missing ligand ACX"></PDBx:pdbx_struct_info> <PDBx:pdbx_struct_info type="nonpolymer_details" value="Disordered ligand geometry for C34 with missing pyridine ring"></PDBx:pdbx_struct_info> <PDBx:pdbx_struct_info type="missing atoms in alternate conformations" value="Y"></PDBx:pdbx_struct_info> </PDBx:pdbx_struct_infoCategory> Additional details about this information item. The information category/type for this item. The value of this information item. Data items in the PDBX_STRUCT_LEGACY_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry. This category provides a container for matrices used to construct icosahedral assemblies in legacy entries. Example 1 - <PDBx:pdbx_struct_legacy_oper_listCategory> <PDBx:pdbx_struct_legacy_oper_list id="2"> <PDBx:matrix11>0.247</PDBx:matrix11> <PDBx:matrix12>0.935</PDBx:matrix12> <PDBx:matrix13>0.256</PDBx:matrix13> <PDBx:matrix21>0.929</PDBx:matrix21> <PDBx:matrix22>0.153</PDBx:matrix22> <PDBx:matrix23>0.337</PDBx:matrix23> <PDBx:matrix31>0.276</PDBx:matrix31> <PDBx:matrix32>0.321</PDBx:matrix32> <PDBx:matrix33>-0.906</PDBx:matrix33> <PDBx:vector1>-8.253</PDBx:vector1> <PDBx:vector2>-11.743</PDBx:vector2> <PDBx:vector3>-1.782</PDBx:vector3> </PDBx:pdbx_struct_legacy_oper_list> </PDBx:pdbx_struct_legacy_oper_listCategory> The [1][1] element of the 3x3 matrix component of the transformation operation. The [1][2] element of the 3x3 matrix component of the transformation operation. The [1][3] element of the 3x3 matrix component of the transformation operation. The [2][1] element of the 3x3 matrix component of the transformation operation. The [2][2] element of the 3x3 matrix component of the transformation operation. The [2][3] element of the 3x3 matrix component of the transformation operation. The [3][1] element of the 3x3 matrix component of the transformation operation. The [3][2] element of the 3x3 matrix component of the transformation operation. The [3][3] element of the 3x3 matrix component of the transformation operation. A descriptive name for the transformation operation. identity matrix two-fold rotation The [1] element of the three-element vector component of the transformation operation. The [2] element of the three-element vector component of the transformation operation. The [3] element of the three-element vector component of the transformation operation. This integer value must uniquely identify a record in the PDBX_STRUCT_LEGACY_OPER_LIST list. Data items in the PDBX_STRUCT_LINK category record details about covalent linkages in the structure. <PDBx:pdbx_struct_linkCategory> <PDBx:pdbx_struct_link id="1"> <PDBx:pdbx_dist_value>2.217</PDBx:pdbx_dist_value> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>CO</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>B12</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>201</PDBx:ptnr1_label_seq_id> <PDBx:ptnr1_symmetry>1_555</PDBx:ptnr1_symmetry> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id>NE2</PDBx:ptnr2_label_atom_id> <PDBx:ptnr2_label_comp_id>HIS</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>16</PDBx:ptnr2_label_seq_id> <PDBx:ptnr2_symmetry>1_555</PDBx:ptnr2_symmetry> <PDBx:type>metalc</PDBx:type> </PDBx:pdbx_struct_link> <PDBx:pdbx_struct_link id="2"> <PDBx:pdbx_dist_value>2.222</PDBx:pdbx_dist_value> <PDBx:ptnr1_label_asym_id>C</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>CO</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>B12</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>201</PDBx:ptnr1_label_seq_id> <PDBx:ptnr1_symmetry>1_555</PDBx:ptnr1_symmetry> <PDBx:ptnr2_label_asym_id>C</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id>NE2</PDBx:ptnr2_label_atom_id> <PDBx:ptnr2_label_comp_id>HIS</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>16</PDBx:ptnr2_label_seq_id> <PDBx:ptnr2_symmetry>1_555</PDBx:ptnr2_symmetry> <PDBx:type>metalc</PDBx:type> </PDBx:pdbx_struct_link> </PDBx:pdbx_struct_linkCategory> Text description of the linkage. The linkage distance in angstroms. A component of the identifier for partner 1 of the structure connection. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure connection. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the atom set specified by attribute ptnr1_label* in category pdbx_struct_link to generate the first partner in the structure connection. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure connection. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Describes the symmetry operation that should be applied to the atom set specified by attribute ptnr2_label* in category pdbx_struct_link to generate the second partner in the structure connection. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The chemical or structural type of the interaction. The value of attribute id in category pdbx_struct_link must uniquely identify a record in the PDBX_STRUCT_LINK list. Data items in the PDBX_STRUCT_MOD_RESIDUE category list the modified polymer components in the entry and provide some details describing the nature of the modification. Example 1 <PDBx:pdbx_struct_mod_residueCategory> <PDBx:pdbx_struct_mod_residue id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>CRW</PDBx:auth_comp_id> <PDBx:auth_seq_id>66</PDBx:auth_seq_id> <PDBx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</PDBx:details> <PDBx:parent_comp_id>ALA</PDBx:parent_comp_id> </PDBx:pdbx_struct_mod_residue> <PDBx:pdbx_struct_mod_residue id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>CRW</PDBx:auth_comp_id> <PDBx:auth_seq_id>66</PDBx:auth_seq_id> <PDBx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</PDBx:details> <PDBx:parent_comp_id>SER</PDBx:parent_comp_id> </PDBx:pdbx_struct_mod_residue> <PDBx:pdbx_struct_mod_residue id="3"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>CRW</PDBx:auth_comp_id> <PDBx:auth_seq_id>66</PDBx:auth_seq_id> <PDBx:details>CIRCULARIZED TRI-PEPTIDE CHROMOPHORE</PDBx:details> <PDBx:parent_comp_id>GLY</PDBx:parent_comp_id> </PDBx:pdbx_struct_mod_residue> </PDBx:pdbx_struct_mod_residueCategory> Part of the identifier for the modified polymer component. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Part of the identifier for the modified polymer component. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier for the modified polymer component. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the modified polymer component. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the modified polymer component. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Details of the modification for this polymer component. Part of the identifier for the modified polymer component. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the modified polymer component. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The parent component identifier for this modified polymer component. The value of attribute id in category pdbx_struct_mod_residue must uniquely identify each item in the PDBX_STRUCT_MOD_RESIDUE list. This is an integer serial number. Data items in the PDBX_STRUCT_MSYM_GEN category record details about the generation of the minimal asymmetric unit. For instance, this category can be used to provide this information for helical and point symmetry systems. The PDBX_STRUCT_MSYM_GEN data items provide the specifications of the components that constitute the asymmetric unit in terms of cartesian transformations of deposited coordinates. Example 1 - <PDBx:pdbx_struct_msym_genCategory> <PDBx:pdbx_struct_msym_gen entity_inst_id="A" msym_id="A" oper_expression="3"></PDBx:pdbx_struct_msym_gen> <PDBx:pdbx_struct_msym_gen entity_inst_id="B" msym_id="B" oper_expression="4"></PDBx:pdbx_struct_msym_gen> <PDBx:pdbx_struct_msym_gen entity_inst_id="B" msym_id="C" oper_expression="5"></PDBx:pdbx_struct_msym_gen> </PDBx:pdbx_struct_msym_genCategory> This data item is a pointer to attribute id in category pdbx_struct_entity_inst in the PDBX_STRUCT_ENTITY_INST category. Uniquely identifies the this structure instance in point symmetry unit. Identifies the operation from category PDBX_STRUCT_OPER_LIST. (1) (1-3) Data items in the PDBX_STRUCT_NCS_VIRUS_GEN category record details about the generation of virus structures from NCS matrix operators. Example 1 <PDBx:pdbx_struct_ncs_virus_genCategory> <PDBx:pdbx_struct_ncs_virus_gen id="1"> <PDBx:asym_id>A</PDBx:asym_id> <PDBx:oper_id>1</PDBx:oper_id> <PDBx:pdb_chain_id>A</PDBx:pdb_chain_id> </PDBx:pdbx_struct_ncs_virus_gen> <PDBx:pdbx_struct_ncs_virus_gen id="2"> <PDBx:asym_id>B</PDBx:asym_id> <PDBx:oper_id>2</PDBx:oper_id> <PDBx:pdb_chain_id>B</PDBx:pdb_chain_id> </PDBx:pdbx_struct_ncs_virus_gen> <PDBx:pdbx_struct_ncs_virus_gen id="3"> <PDBx:asym_id>C</PDBx:asym_id> <PDBx:oper_id>3</PDBx:oper_id> <PDBx:pdb_chain_id>C</PDBx:pdb_chain_id> </PDBx:pdbx_struct_ncs_virus_gen> </PDBx:pdbx_struct_ncs_virus_genCategory> The NCS operation is applied to the component of the asymmetric unit identified by this id. A Identifies the NCS operation (_struct_ncs_oper.id) 1 The NCS operation is applied to the chain identified by this id. A Unique id for generator. 1 Data items in the PDBX_STRUCT_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry. Example 1 - <PDBx:pdbx_struct_oper_listCategory> <PDBx:pdbx_struct_oper_list id="2"> <PDBx:matrix11>0.247</PDBx:matrix11> <PDBx:matrix12>0.935</PDBx:matrix12> <PDBx:matrix13>0.256</PDBx:matrix13> <PDBx:matrix21>0.929</PDBx:matrix21> <PDBx:matrix22>0.153</PDBx:matrix22> <PDBx:matrix23>0.337</PDBx:matrix23> <PDBx:matrix31>0.276</PDBx:matrix31> <PDBx:matrix32>0.321</PDBx:matrix32> <PDBx:matrix33>-0.906</PDBx:matrix33> <PDBx:type>point symmetry operation</PDBx:type> <PDBx:vector1>-8.253</PDBx:vector1> <PDBx:vector2>-11.743</PDBx:vector2> <PDBx:vector3>-1.782</PDBx:vector3> </PDBx:pdbx_struct_oper_list> </PDBx:pdbx_struct_oper_listCategory> The [1][1] element of the 3x3 matrix component of the transformation operation. The [1][2] element of the 3x3 matrix component of the transformation operation. The [1][3] element of the 3x3 matrix component of the transformation operation. The [2][1] element of the 3x3 matrix component of the transformation operation. The [2][2] element of the 3x3 matrix component of the transformation operation. The [2][3] element of the 3x3 matrix component of the transformation operation. The [3][1] element of the 3x3 matrix component of the transformation operation. The [3][2] element of the 3x3 matrix component of the transformation operation. The [3][3] element of the 3x3 matrix component of the transformation operation. A descriptive name for the transformation operation. 1_555 two-fold rotation The symmetry operation corresponding to the transformation operation. x,y,z x+1/2,y,-z A code to indicate the type of operator. The [1] element of the three-element vector component of the transformation operation. The [2] element of the three-element vector component of the transformation operation. The [3] element of the three-element vector component of the transformation operation. This identifier code must uniquely identify a record in the PDBX_STRUCT_OPER_LIST list. Data items in the PDBX_STRUCT_OPER_LIST_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_OPER_LIST. Example 1 - <PDBx:pdbx_struct_oper_list_depositor_infoCategory> <PDBx:pdbx_struct_oper_list_depositor_info id="2"> <PDBx:matrix11>0.247</PDBx:matrix11> <PDBx:matrix12>0.935</PDBx:matrix12> <PDBx:matrix13>0.256</PDBx:matrix13> <PDBx:matrix21>0.929</PDBx:matrix21> <PDBx:matrix22>0.153</PDBx:matrix22> <PDBx:matrix23>0.337</PDBx:matrix23> <PDBx:matrix31>0.276</PDBx:matrix31> <PDBx:matrix32>0.321</PDBx:matrix32> <PDBx:matrix33>-0.906</PDBx:matrix33> <PDBx:type>point symmetry operation</PDBx:type> <PDBx:vector1>-8.253</PDBx:vector1> <PDBx:vector2>-11.743</PDBx:vector2> <PDBx:vector3>-1.782</PDBx:vector3> </PDBx:pdbx_struct_oper_list_depositor_info> </PDBx:pdbx_struct_oper_list_depositor_infoCategory> The [1][1] element of the 3x3 matrix component of the transformation operation. The [1][2] element of the 3x3 matrix component of the transformation operation. The [1][3] element of the 3x3 matrix component of the transformation operation. The [2][1] element of the 3x3 matrix component of the transformation operation. The [2][2] element of the 3x3 matrix component of the transformation operation. The [2][3] element of the 3x3 matrix component of the transformation operation. The [3][1] element of the 3x3 matrix component of the transformation operation. The [3][2] element of the 3x3 matrix component of the transformation operation. The [3][3] element of the 3x3 matrix component of the transformation operation. A descriptive name for the transformation operation. 1_555 two-fold rotation The symmetry operation corresponding to the transformation operation. x,y,z x+1/2,y,-z A code to indicate the type of operator. The [1] element of the three-element vector component of the transformation operation. The [2] element of the three-element vector component of the transformation operation. The [3] element of the three-element vector component of the transformation operation. This identifier code must uniquely identify a record in the PDBX_STRUCT_OPER_LIST_DEPOSITOR_INFO list. Data items in the PDBX_STRUCT_PACK_GEN category record details about the generation of the packing picture(s). Example 1 - based on NDB entry ADJ066 <PDBx:pdbx_struct_pack_genCategory> <PDBx:pdbx_struct_pack_gen asym_id="A" id="1" symmetry="1_555"> <PDBx:color_blue>.4</PDBx:color_blue> <PDBx:color_green>.3</PDBx:color_green> <PDBx:color_red>.2</PDBx:color_red> </PDBx:pdbx_struct_pack_gen> </PDBx:pdbx_struct_pack_genCategory> Gives rgb color code in order to produce atlas entry packing picture. 0.6 Gives rgb color code in order to produce atlas entry packing picture. 0.6 Gives rgb color code in order to produce atlas entry packing picture. 0.6 Crystal type Packing type This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. Ordinal identifier Describes the symmetry operation that should be applied to the atom set specified by attribute asym_id in category pdbx_struct_pack_gen to generate a packing picture. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate deletions in the sequence of the entity described in the referenced database entry. Example 1 <PDBx:pdbx_struct_ref_seq_deletionCategory> <PDBx:pdbx_struct_ref_seq_deletion id="1"> <PDBx:asym_id>A</PDBx:asym_id> <PDBx:comp_id>LEU</PDBx:comp_id> <PDBx:db_code>P15456</PDBx:db_code> <PDBx:db_name>UNP</PDBx:db_name> <PDBx:db_seq_id>23</PDBx:db_seq_id> <PDBx:details xsi:nil="true" /> </PDBx:pdbx_struct_ref_seq_deletion> <PDBx:pdbx_struct_ref_seq_deletion id="1"> <PDBx:asym_id>A</PDBx:asym_id> <PDBx:comp_id>THR</PDBx:comp_id> <PDBx:db_code>P15456</PDBx:db_code> <PDBx:db_name>UNP</PDBx:db_name> <PDBx:db_seq_id>24</PDBx:db_seq_id> <PDBx:details xsi:nil="true" /> </PDBx:pdbx_struct_ref_seq_deletion> <PDBx:pdbx_struct_ref_seq_deletion id="1"> <PDBx:asym_id>A</PDBx:asym_id> <PDBx:comp_id>GLN</PDBx:comp_id> <PDBx:db_code>P15456</PDBx:db_code> <PDBx:db_name>UNP</PDBx:db_name> <PDBx:db_seq_id>25</PDBx:db_seq_id> <PDBx:details xsi:nil="true" /> </PDBx:pdbx_struct_ref_seq_deletion> </PDBx:pdbx_struct_ref_seq_deletionCategory> Identifies the polymer entity instance in this entry corresponding to the reference sequence in which the deletion is specified. This data item is a pointer to attribute asym_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. The monomer name found at this position in the referenced database entry. The code for this entity or biological unit or for a closely related entity or biological unit in the named database. The name of the database containing reference information about this entity or biological unit. This data item is the database sequence numbering of the deleted residue A description of any special aspects of the deletion The value of attribute id in category pdbx_struct_ref_seq_deletion must uniquely identify a record in the PDBX_STRUCT_REF_SEQ_DELETION list. Data items in the PDBX_STRUCT_REF_SEQ_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ. Example 1 - <PDBx:pdbx_struct_ref_seq_depositor_infoCategory> <PDBx:pdbx_struct_ref_seq_depositor_info ref_id="1"> <PDBx:db_accession xsi:nil="true" /> <PDBx:db_align_beg>18</PDBx:db_align_beg> <PDBx:db_align_end>276</PDBx:db_align_end> <PDBx:db_code xsi:nil="true" /> <PDBx:db_name xsi:nil="true" /> <PDBx:db_seq_one_letter_code xsi:nil="true" /> <PDBx:details xsi:nil="true" /> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:seq_align_begin xsi:nil="true" /> <PDBx:seq_align_end xsi:nil="true" /> </PDBx:pdbx_struct_ref_seq_depositor_info> </PDBx:pdbx_struct_ref_seq_depositor_infoCategory> Accession code of the reference database. P07617 The sequence position in the referenced database entry at which the alignment begins. The sequence position in the referenced database entry at which the alignment ends. The code for this entity or biological unit or for a closely related entity or biological unit in the named database. 1ABC ABCDEF The name of the database containing reference information about this entity or biological unit. UNP GB Database chemical sequence expressed as string of one-letter residue codes. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other A description of special aspects of the sequence alignment. This data item is a pointer to attribute id in category entity in the ENTITY category. Beginning index in the author provided chemical sequence. 1 2 Ending index in the author provided chemical sequence. 201 451 This data item is a unique identifier for reference sequence information. Data items in the PDBX_STRUCT_REF_SEQ_DIF_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ_DIF. Example 1 - <PDBx:pdbx_struct_ref_seq_dif_depositor_infoCategory> <PDBx:pdbx_struct_ref_seq_dif_depositor_info ordinal="1"> <PDBx:auth_mon_id>ALA</PDBx:auth_mon_id> <PDBx:auth_seq_id>181</PDBx:auth_seq_id> <PDBx:db_mon_id>GLU</PDBx:db_mon_id> <PDBx:db_seq_id>301</PDBx:db_seq_id> <PDBx:details xsi:nil="true" /> <PDBx:ref_id>1</PDBx:ref_id> </PDBx:pdbx_struct_ref_seq_dif_depositor_info> </PDBx:pdbx_struct_ref_seq_dif_depositor_infoCategory> The description of the sequence difference. The monomer type found at this position in the sequence of the entity or biological unit provided by the depositor. The monomer position in the author provided sequence. Accession code of the reference database. P07617 The code for this entity or biological unit or for a closely related entity or biological unit in the named database. 1ABC ABCDEF The monomer type found at this position in the referenced database entry. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The name of the database containing reference information about this entity or biological unit. PDB UniProt Genbank The monomer position in the referenced database entry. A description of special aspects of the point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute ref_id in category struct_ref_seq in the STRUCT_REF_SEQ_DEPOSITOR_INFO category. Ordinal index for this category. Data items in the PDBX_STRUCT_REF_SEQ_FEATURE category provide a mechanism for identifying and annotating sequence features. Example 1 - <PDBx:pdbx_struct_ref_seq_featureCategory> <PDBx:pdbx_struct_ref_seq_feature feature_id="1"> <PDBx:align_id>algn2</PDBx:align_id> <PDBx:beg_auth_mon_id>GLU</PDBx:beg_auth_mon_id> <PDBx:beg_auth_seq_id>10</PDBx:beg_auth_seq_id> <PDBx:details> Special</PDBx:details> <PDBx:end_auth_mon_id>PHE</PDBx:end_auth_mon_id> <PDBx:end_auth_seq_id>14</PDBx:end_auth_seq_id> <PDBx:type>variant</PDBx:type> </PDBx:pdbx_struct_ref_seq_feature> </PDBx:pdbx_struct_ref_seq_featureCategory> This data item is a pointer to attribute align_id in category struct_ref_seq in the STRUCT_REF_SEQ category. Instance identifier for the polymer molecule. A B Monomer ID at the initial position in the PDB sequence segment. 1 2 Initial position in the PDB sequence segment. 1 2 Initial insertion code of the PDB sequence segment. A B Initial position in the sequence segment. 1 2 A description of special aspects of the feature Monomer ID at the terminal position in the PDB sequence segment 1 2 Ending position in the PDB sequence segment 1 2 Terminal insertion code of the PDB sequence segment. A B Ending position in the sequence segment 1 2 PDB strand/chain id. A B A classification of the feature Uniquely identfies a sequence feature in the STRUCT_REF_SEQ_FEATURE category. Data items in the PDBX_STRUCT_REF_SEQ_FEATURE_PROP category provide a mechanism for identifying and annotating properties of sequence features. Example 1 - <PDBx:pdbx_struct_ref_seq_feature_propCategory> <PDBx:pdbx_struct_ref_seq_feature_prop feature_id="1" property_id="1"> <PDBx:beg_db_mon_id>GLU</PDBx:beg_db_mon_id> <PDBx:beg_db_seq_id>100</PDBx:beg_db_seq_id> <PDBx:details> Special splice at ...</PDBx:details> <PDBx:end_db_mon_id>PHE</PDBx:end_db_mon_id> <PDBx:end_db_seq_id>104</PDBx:end_db_seq_id> <PDBx:type>VARIABLE_SPLICING</PDBx:type> <PDBx:value>VSP_003456</PDBx:value> </PDBx:pdbx_struct_ref_seq_feature_prop> </PDBx:pdbx_struct_ref_seq_feature_propCategory> The begining monomer type found at the starting position in the referenced database entry. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The begining monomer sequence position in the referenced database entry. A description of special aspects of the property value pair. The terminal monomer type found at the ending position in the referenced database entry. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The terminal monomer sequence position in the referenced database entry. Property type. deletion', 'expression tag', 'variant', 'other Property value. This data item is a pointer to attribute feature_id in category pdbx_struct_ref_seq_feature in the STRUCT_REF_SEQ_FEATURE category. This uniquely identifies the a property of a sequence feature in the STRUCT_REF_SEQ_FEATURE_PROPx category. Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate insertions in the sequence of the entity described in the referenced database entry. Example 1 <PDBx:pdbx_struct_ref_seq_insertionCategory> <PDBx:pdbx_struct_ref_seq_insertion id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:asym_id>A</PDBx:asym_id> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_seq_id>104</PDBx:auth_seq_id> <PDBx:comp_id>GLY</PDBx:comp_id> <PDBx:db_code>P00752</PDBx:db_code> <PDBx:db_name>UNP</PDBx:db_name> <PDBx:details>INSERTION</PDBx:details> <PDBx:seq_id>102</PDBx:seq_id> </PDBx:pdbx_struct_ref_seq_insertion> <PDBx:pdbx_struct_ref_seq_insertion id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:asym_id>A</PDBx:asym_id> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_seq_id>105</PDBx:auth_seq_id> <PDBx:comp_id>TRP</PDBx:comp_id> <PDBx:db_code>P00752</PDBx:db_code> <PDBx:db_name>UNP</PDBx:db_name> <PDBx:details>INSERTION</PDBx:details> <PDBx:seq_id>103</PDBx:seq_id> </PDBx:pdbx_struct_ref_seq_insertion> </PDBx:pdbx_struct_ref_seq_insertionCategory> Part of the author identifier of the inserted residue. This data item is a pointer to attribute pdb_ins_code in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. Part of the identifier of the inserted residue. This data item is a pointer to attribute asym_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. Part of the author identifier of the inserted residue. This data item is a pointer to attribute pdb_strand_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. Part of the author identifier of the inserted residue. This data item is a pointer to attribute auth_seq_num in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. Part of the identifier of the inserted residue. This data item is a pointer to attribute mon_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. The code for this entity or biological unit or for a closely related entity or biological unit in the named database. The name of the database containing reference information about this entity or biological unit. A description of any special aspects of the insertion Part of the author identifier of the inserted residue. This data item is a pointer to attribute seq_id in category pdbx_poly_seq_scheme in the PDBX_POLY_SEQ_SCHEME category. The value of attribute id in category pdbx_struct_ref_seq_insertion must uniquely identify a record in the PDBX_STRUCT_REF_SEQ_INSERTION list. Data items in the PDBX_STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta sheet. This category is provided for cases where only a single hydrogen bond is used to register the two residue ranges. Category STRUCT_SHEET_HBOND should be used when the initial and terminal hydrogen bonds for strand pair are known. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the first partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the residue identifier for the second partner of the registration hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. Data items in the PDBX_STRUCT_SPECIAL_SYMMETRY category list the molecular components that lie on special symmetry positions. Example 1 <PDBx:pdbx_struct_special_symmetryCategory> <PDBx:pdbx_struct_special_symmetry id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>Q</PDBx:auth_asym_id> <PDBx:auth_comp_id>ATP</PDBx:auth_comp_id> <PDBx:auth_seq_id>412</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> </PDBx:pdbx_struct_special_symmetry> </PDBx:pdbx_struct_special_symmetryCategory> Part of the identifier for the molecular component. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Part of the identifier for the molecular component. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier for the molecular component. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the molecular component. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the molecular component. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier for the molecular component. This data item is a pointer to attribute label_alt.id in category atom_site in the ATOM_SITE category. Part of the identifier for the molecular component. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the molecular component. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the molecular component. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The value of attribute id in category pdbx_struct_special_symmetry must uniquely identify each item in the PDBX_STRUCT_SPECIAL_SYMMETRY list. This is an integer serial number. Data items in the PDBX_SUGAR_PHOSPHATE_GEOMETRY record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards. Example 1 - <PDBx:pdbx_sugar_phosphate_geometryCategory> <PDBx:pdbx_sugar_phosphate_geometry id="1"> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_seq_id>1</PDBx:auth_seq_id> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>A</PDBx:label_comp_id> <PDBx:label_seq_id>1</PDBx:label_seq_id> <PDBx:model_id xsi:nil="true" /> <PDBx:o3_p_o5_c5>140.1</PDBx:o3_p_o5_c5> </PDBx:pdbx_sugar_phosphate_geometry> </PDBx:pdbx_sugar_phosphate_geometryCategory> This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The c1_c2 covalent element of this monomer. The c1_c2_c3 covalent element of this monomer. The c1_c2_c3_c4 covalent element of this monomer. The c1_n1_9_c2_4 covalent element of this monomer. The c1_n1_9_c6_8 covalent element of this monomer. The c1_n9_1 covalent element of this monomer. The c2_c1_n1_9 covalent element of this monomer. The c2_c3 covalent element of this monomer. The c2_c3_c4 covalent element of this monomer. The c2_c3_c4_o4 covalent element of this monomer. The c2_c3_o3 covalent element of this monomer. The c3_c4 covalent element of this monomer. The c3_c4_o4 covalent element of this monomer. The c3_c4_o4_c1 covalent element of this monomer. The c3_o3 covalent element of this monomer. The c3_o3_p covalent element of this monomer. The c3_o3_p_o5 covalent element of this monomer. The c4_c3_o3 covalent element of this monomer. The c4_c3_o3_p covalent element of this monomer. The c4_o4 covalent element of this monomer. The c4_o4_c1 covalent element of this monomer. The c4_o4_c1_c2 covalent element of this monomer. The c4_o4_c1_n1_9 covalent element of this monomer. The c5_c4 covalent element of this monomer. The c5_c4_c3 covalent element of this monomer. The c5_c4_c3_c2 covalent element of this monomer. The c5_c4_c3_o3 covalent element of this monomer. The c5_c4_o4 covalent element of this monomer. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The maximum torsion value sigma-m, c1_c2_c3_c4/cos(P) of this monomer. The model number The n1_c2 covalent element of this monomer. The n1_c6 covalent element of this monomer. The n9_c4 covalent element of this monomer. The n9_c8 covalent element of this monomer. Neighbor component in the 3' direction. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Neighbor component in the 5' direction. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. The next_c3_o3_p_o5 covalent element of this monomer. The next_c4_c3_o3_p covalent element of this monomer. The next_c4_o4_c1_n1_9 covalent element of this monomer. The next_c5_c4_c3_o3 covalent element of this monomer. The next_label_comp_id covalent element of this monomer. The next_label_seq_id covalent element of this monomer. The next_o3_p_o5_c5 covalent element of this monomer. The next_o4_c1_n1_9_c2_4 covalent element of this monomer. The next_o5_c5_c4_c3 covalent element of this monomer. The next_p_o5_c5_c4 covalent element of this monomer. The o1p_p_o2p covalent element of this monomer. The o3_c3_c2_o2 covalent element of this monomer. The o3_p covalent element of this monomer. The o3_p_o5 covalent element of this monomer. The o3_p_o5_c5 covalent element of this monomer. The o4_c1 covalent element of this monomer. The o4_c1_c2 covalent element of this monomer. The o4_c1_c2_c3 covalent element of this monomer. The o4_c1_n1_9 covalent element of this monomer. The o4_c1_n1_9_c2_4 covalent element of this monomer. The o4_c1_n1_9_c6_8 covalent element of this monomer. The o4_c4_c3_o3 covalent element of this monomer. The o5_c5 covalent element of this monomer. The o5_c5_c4 covalent element of this monomer. The o5_c5_c4_c3 covalent element of this monomer. The o5_c5_c4_o4 covalent element of this monomer. The p_o1p covalent element of this monomer. The p_o2p covalent element of this monomer. The p_o5 covalent element of this monomer. The p_o5_c5 covalent element of this monomer. The p_o5_c5_c4 covalent element of this monomer. The pseudo rotation angle of this monomer. The value of attribute id in category pdbx_sugar_phosphate_geometry must uniquely identify each item in the PDBX_SUGAR_PHOSPHATE_GEOMETRY list. This is an integer serial number. Container category for a list of feature flags associated with each structure entry. A feature flag value Entry ID. A feature flag name. Data items in the PDBX_SUPPORTING_EXP_DATA_SET category record to experimental data set dependencies for this entry. Example 1 - <PDBx:pdbx_supporting_exp_data_setCategory> <PDBx:pdbx_supporting_exp_data_set ordinal="1"> <PDBx:data_content_type>X-ray structure factor amplitudes</PDBx:data_content_type> <PDBx:data_version_major>1</PDBx:data_version_major> <PDBx:data_version_minor>2</PDBx:data_version_minor> </PDBx:pdbx_supporting_exp_data_set> </PDBx:pdbx_supporting_exp_data_setCategory> The type of the experimenatal data set. X-ray structure factor amplitudes NMR chemical shifts NMR restraints The major version on data of the experimental data content on which this entry depends. 2 1 The major version on data of the experimental data content on which this entry depends. 1 2 Additional details describing the content of the supporting data set and its application to the current investigation. Ordinal identifier for each experimental data set. <PDBx:pdbx_tableinfoCategory> <PDBx:pdbx_tableinfo tablename="summary"> <PDBx:WWW_Report_Criteria>1</PDBx:WWW_Report_Criteria> <PDBx:WWW_Selection_Criteria>1</PDBx:WWW_Selection_Criteria> <PDBx:description>summary data</PDBx:description> <PDBx:group_name>STRUCTURE</PDBx:group_name> <PDBx:table_serial_no>1</PDBx:table_serial_no> <PDBx:type>1</PDBx:type> </PDBx:pdbx_tableinfo> </PDBx:pdbx_tableinfoCategory> SQL table visibility in WWW reports queries. 0=no, 1=yes SQL table visibility in WWW selection querires. 0=no, 1=yes SQL table description. Table of solvent coordinates SQL table group name.. STRUCTURE FEATURES, SOURCE ORGANISM SQL table serial number. 1,2,3,4,... SQL table type. 0=general, 1=coordinate, 2=derived, 3=schema SQL table name. structure_summary Data items in the PDBX_TRNA_INFO category are still used until the 'entity' categories are entered into the database, even though the T-RNA is repeated. Example 1 - based on NDB entry TRNA04 <PDBx:pdbx_trna_infoCategory> <PDBx:pdbx_trna_info id="1"> <PDBx:name>Yeast Phenylalanine T-RNA</PDBx:name> <PDBx:num_per_asym_unit>1</PDBx:num_per_asym_unit> </PDBx:pdbx_trna_info> </PDBx:pdbx_trna_infoCategory> Name of trna. Yeast Phenylalanine T-RNA Number of trna molecules per asymmetric unit. 1 Serial number. 1 Data items in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS category list the atoms within the entry that are either unobserved or have zero occupancy/ Example 1 <PDBx:pdbx_unobs_or_zero_occ_atomsCategory> <PDBx:pdbx_unobs_or_zero_occ_atoms id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>CG</PDBx:auth_atom_id> <PDBx:auth_comp_id>ARG</PDBx:auth_comp_id> <PDBx:auth_seq_id>412</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>Y</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_atoms> <PDBx:pdbx_unobs_or_zero_occ_atoms id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>CD</PDBx:auth_atom_id> <PDBx:auth_comp_id>ARG</PDBx:auth_comp_id> <PDBx:auth_seq_id>412</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>Y</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_atoms> <PDBx:pdbx_unobs_or_zero_occ_atoms id="3"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>NE</PDBx:auth_atom_id> <PDBx:auth_comp_id>ARG</PDBx:auth_comp_id> <PDBx:auth_seq_id>412</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>Y</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_atoms> <PDBx:pdbx_unobs_or_zero_occ_atoms id="4"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>CZ</PDBx:auth_atom_id> <PDBx:auth_comp_id>ARG</PDBx:auth_comp_id> <PDBx:auth_seq_id>412</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>Y</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_atoms> <PDBx:pdbx_unobs_or_zero_occ_atoms id="5"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>NH1</PDBx:auth_atom_id> <PDBx:auth_comp_id>ARG</PDBx:auth_comp_id> <PDBx:auth_seq_id>412</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>Y</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_atoms> <PDBx:pdbx_unobs_or_zero_occ_atoms id="6"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_atom_id>NH2</PDBx:auth_atom_id> <PDBx:auth_comp_id>ARG</PDBx:auth_comp_id> <PDBx:auth_seq_id>412</PDBx:auth_seq_id> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>Y</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_atoms> </PDBx:pdbx_unobs_or_zero_occ_atomsCategory> Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_alt.id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy atom. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The value of occupancy flag indicates whether the atom is either unobserved (=1) or has zero occupancy (=0) The value of polymer flag indicates whether the unobserved or zero occupancy atom is part of a polymer chain The value of attribute id in category pdbx_unobs_or_zero_occ_atoms must uniquely identify each item in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS list. This is an integer serial number. Data items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the residues within the entry that are not observed or have zero occupancy. Example 1 <PDBx:pdbx_unobs_or_zero_occ_residuesCategory> <PDBx:pdbx_unobs_or_zero_occ_residues id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>B</PDBx:auth_asym_id> <PDBx:auth_comp_id>VAL</PDBx:auth_comp_id> <PDBx:auth_seq_id>36</PDBx:auth_seq_id> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>Y</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_residues> <PDBx:pdbx_unobs_or_zero_occ_residues id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>B</PDBx:auth_asym_id> <PDBx:auth_comp_id>ARG</PDBx:auth_comp_id> <PDBx:auth_seq_id>108</PDBx:auth_seq_id> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>Y</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_residues> <PDBx:pdbx_unobs_or_zero_occ_residues id="3"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>D</PDBx:auth_asym_id> <PDBx:auth_comp_id>PPI</PDBx:auth_comp_id> <PDBx:auth_seq_id>438</PDBx:auth_seq_id> <PDBx:occupancy_flag>1</PDBx:occupancy_flag> <PDBx:polymer_flag>N</PDBx:polymer_flag> </PDBx:pdbx_unobs_or_zero_occ_residues> </PDBx:pdbx_unobs_or_zero_occ_residuesCategory> Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier for the unobserved or zero occupancy residue. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The value of occupancy flag indicates whether the residue is unobserved (= 1) or the coordinates have an occupancy of zero (=0) The value of polymer flag indicates whether the unobserved or zero occupancy residue is part of a polymer chain or not The value of attribute id in category pdbx_unobs_or_zero_occ_residues must uniquely identify each item in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES list. This is an integer serial number. These records give information about residues which do not pair (h-bond) in the asymmetric unit. The records about Watson-Crick base pairing depend on these records. Example 1 - based on NDB entry PDR001 <PDBx:pdbx_unpairCategory> <PDBx:pdbx_unpair chain_id="A"> <PDBx:residue_name>A</PDBx:residue_name> <PDBx:residue_number>1</PDBx:residue_number> </PDBx:pdbx_unpair> <PDBx:pdbx_unpair chain_id="B"> <PDBx:residue_name>T</PDBx:residue_name> <PDBx:residue_number>21</PDBx:residue_number> </PDBx:pdbx_unpair> </PDBx:pdbx_unpairCategory> Name of residue which does not pair. G U Number of residue which does not pair. 1 2 Strand id. A B The PDBX_VAL_ANGLE category lists the covalent bond angles in this entry deviating by greater than 6*sigma from standard values. This is a completely derived category. Do not edit. Value of the angle deviating by more than 6*RMSD from the expected dictionary value. Value of the deviation (in degrees) from 6*RMSD for the angle bounded by the three sites from the expected dictionary value Optional identifier of the first of the three atom sites that define the angle. Optional identifier of the second of the three atom sites that define the angle. Optional identifier of the third of the three atom sites that define the angle. Identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the angle connection. A component of the identifier for partner 2 of the angle connection. A component of the identifier for partner 3 of the angle connection. A component of the identifier for partner 1 of the angle connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the angle connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the angle connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the angle connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 2 of the angle connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 3 of the angle connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 1 of the angle connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the angle connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the angle connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the angle connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the angle connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 3 of the angle connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number for the given angle The value of attribute id in category pdbx_val_angle must uniquely identify each item in the PDBX_VAL_ANGLE list. This is an integer serial number. The PDBX_VAL_BOND category lists the covalent bond angles in this entry deviating by greater than 6*sigma from standard values. This is a completely derived category. Do not edit. Optional identifier of the first of the two atom sites that define the covalent bond. Optional identifier of the second of the two atom sites that define the covalent bond. identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the bond distance deviating by more than 6*RMSD from the standard dictionary value. The value of the deviation from ideal for the defined covalent bond for the two atoms defined. A component of the identifier for partner 1 of the bond connection. A component of the identifier for partner 2 of the bond connection. A component of the identifier for partner 1 of the bond connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the bond connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the bond connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 2 of the bond connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 1 of the bond connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the bond connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the bond connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the bond connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number for the given bond The value of attribute id in category pdbx_val_bond must uniquely identify each item in the PDBX_VAL_BOND list. This is an integer serial number. Data items in the PDBX_VAL_CHIRAL category list the atoms with nonstandard chiralities. This is a completely derived category. Do not edit. Identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Identifier of chiral center atom alt ID. Identifier of chiral center atom. Identifier of chiral neighbor alt ID. Identifier of chiral neighbor atom. Identifier of the residue. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. Identifier of the residue. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number for the given residue The value of attribute id in category pdbx_val_chiral must uniquely identify each item in the PDBX_VAL_CHIRAL list. This is an integer serial number. The PDBX_VAL_CONTACT category lists non-bonded atoms within the assymetric unit of the entry that are in close contact. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstrom is used. This is a completely derived category. Do not edit. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the close contact for the two atoms defined. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number for the given angle The value of attribute id in category pdbx_val_contact must uniquely identify each item in the PDBX_VAL_CONTACT list. This is an integer serial number. The PDBX_VAL_SYM_CONTACT category lists symmetry related contacts amoung non-bonded atoms. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstrom is used. This is a completely derived category. Do not edit. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the close contact for the two atoms defined. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the close contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the close contact. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The model number for the given angle The symmetry operation applied to the first of the two atoms defining the close contact. The Symmetry equivalent position is given in the 'xyz' representation. The symmetry operation applied to the second of the two atoms defining the close contact. The Symmetry equivalent position is given in the 'xyz' representation. The value of attribute id in category pdbx_val_sym_contact must uniquely identify each item in the PDBX_VAL_SYM_CONTACT list. This is an integer serial number. Data items in the PDBX_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centers. IMPROPER HA N C CB chirality CA IMPROPER HB1 HB2 CA CG stereo CB as this number approaches (+) or (-) 180.0, then the error in predicting the true chirality of the center increases. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. HERE improper C---N----CA---CB done expected answer is around -120 mean -122.52 D-amino acid is +120.0 Example 1 <PDBx:pdbx_validate_chiralCategory> <PDBx:pdbx_validate_chiral id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id>ASP</PDBx:auth_asym_id> <PDBx:auth_comp_id>B</PDBx:auth_comp_id> <PDBx:auth_seq_id>405</PDBx:auth_seq_id> <PDBx:details>ALPHA-CARBON</PDBx:details> <PDBx:omega>150.48</PDBx:omega> </PDBx:pdbx_validate_chiral> </PDBx:pdbx_validate_chiralCategory> Optional identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the given residue This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A description of the outlier angle e.g. ALPHA-CARBON Part of the identifier of the residue This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The value of the OMEGA angle for the peptide linkage between the two defined residues The value of attribute id in category pdbx_validate_chiral must uniquely identify each item in the PDBX_VALIDATE_CHIRAL list. This is an integer serial number. Data items in the PDBX_VALIDATE_CLOSE_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Contacts within the asymmetric unit are considered. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstroms is used. Example 1 <PDBx:pdbx_validate_close_contactCategory> <PDBx:pdbx_validate_close_contact id="1"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id_1>B</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>B</PDBx:auth_asym_id_2> <PDBx:auth_atom_id_1 xsi:nil="true" /> <PDBx:auth_atom_id_2 xsi:nil="true" /> <PDBx:auth_comp_id_1>VAL</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>ARG</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>36</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>108</PDBx:auth_seq_id_2> <PDBx:dist>2.16</PDBx:dist> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> </PDBx:pdbx_validate_close_contact> <PDBx:pdbx_validate_close_contact id="2"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id_1>B</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>B</PDBx:auth_asym_id_2> <PDBx:auth_atom_id_1 xsi:nil="true" /> <PDBx:auth_atom_id_2 xsi:nil="true" /> <PDBx:auth_comp_id_1>ARG</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>VAL</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>108</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>36</PDBx:auth_seq_id_2> <PDBx:dist>2.16</PDBx:dist> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> </PDBx:pdbx_validate_close_contact> </PDBx:pdbx_validate_close_contactCategory> Optional identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Optional identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the given contact Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the close contact for the two atoms defined. An optional identifier of the first of the two atoms that define the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atoms that define the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The symmetry of the first of the two atoms define the close contact. The Symmetry equivalent position is given in the 'xyz' representation. The symmetry of the second of the two atoms define the close contact. The Symmetry equivalent position is given in the 'xyz' representation. The value of attribute id in category pdbx_validate_close_contact must uniquely identify each item in the PDBX_VALIDATE_CLOSE_CONTACT list. This is an integer serial number. Data items in the PDBX_VALIDATE_MAIN_CHAIN_PLANE category list the residues that contain unexpected deviations from planes for main chain atoms as defined by the improper torsion angle describing planarity: PLANARITY = C(i-1) - CA(i-1) - N(i) - O(i-1) ==> planar < 5 as a pseudo torsion Example 1 <PDBx:pdbx_validate_main_chain_planeCategory> <PDBx:pdbx_validate_main_chain_plane id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id>G</PDBx:auth_asym_id> <PDBx:auth_comp_id>TRP</PDBx:auth_comp_id> <PDBx:auth_seq_id>20</PDBx:auth_seq_id> <PDBx:improper_torsion_angle>29.901</PDBx:improper_torsion_angle> </PDBx:pdbx_validate_main_chain_plane> <PDBx:pdbx_validate_main_chain_plane id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id>G</PDBx:auth_asym_id> <PDBx:auth_comp_id>TRP</PDBx:auth_comp_id> <PDBx:auth_seq_id>21</PDBx:auth_seq_id> <PDBx:improper_torsion_angle>-42.450</PDBx:improper_torsion_angle> </PDBx:pdbx_validate_main_chain_plane> </PDBx:pdbx_validate_main_chain_planeCategory> Optional identifier of the residue in which the plane is calculated This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the residue in which the plane is calculated This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value for the torsion angle C(i-1) - CA(i-1) - N(i) - O(i-1) Optional identifier of the residue in which the plane is calculated This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The value of attribute id in category pdbx_validate_main_chain_plane must uniquely identify each item in the PDBX_VALIDATE_MAIN_CHAIN_PLANE list. This is an integer serial number. Data items in the PDBX_VALIDATE_PEPTIDE_OMEGA category list the residues that contain peptide bonds deviate significantly from both cis and trans conformation. cis bonds, if any, are listed on cispep records. trans is defined as 180 +/- 30 and cis is defined as 0 +/- 30 degrees. Example 1 <PDBx:pdbx_validate_peptide_omegaCategory> <PDBx:pdbx_validate_peptide_omega id="1"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id_1>ASP</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>ARG</PDBx:auth_asym_id_2> <PDBx:auth_comp_id_1>A</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>A</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>414</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>413</PDBx:auth_seq_id_2> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> <PDBx:omega>147.84</PDBx:omega> </PDBx:pdbx_validate_peptide_omega> <PDBx:pdbx_validate_peptide_omega id="2"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id_1>ASN</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>ALA</PDBx:auth_asym_id_2> <PDBx:auth_comp_id_1>B</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>B</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>289</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>288</PDBx:auth_seq_id_2> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> <PDBx:omega>-39.12</PDBx:omega> </PDBx:pdbx_validate_peptide_omega> </PDBx:pdbx_validate_peptide_omegaCategory> Optional identifier of the first residue in the bond This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Optional identifier of the second residue in the bond This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the given residue This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier of the first residue in the bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second residue in the bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first residue in the bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second residue in the bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first residue in the bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second residue in the bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Optional identifier of the first residue in the torsion angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. Optional identifier of the second residue in the torsion angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The value of the OMEGA angle for the peptide linkage between the two defined residues The value of attribute id in category pdbx_validate_peptide_omega must uniquely identify each item in the PDBX_VALIDATE_PEPTIDE_OMEGA list. This is an integer serial number. Data items in the PDBX_VALIDATE_PLANES category list the residues that contain unexpected deviations from planes centers. Example 1 <PDBx:pdbx_validate_planesCategory> <PDBx:pdbx_validate_planes id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>DG</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:rmsd>0.068</PDBx:rmsd> <PDBx:type>SIDE CHAIN</PDBx:type> </PDBx:pdbx_validate_planes> <PDBx:pdbx_validate_planes id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>DT</PDBx:auth_comp_id> <PDBx:auth_seq_id>4</PDBx:auth_seq_id> <PDBx:rmsd>0.198</PDBx:rmsd> <PDBx:type>SIDE CHAIN</PDBx:type> </PDBx:pdbx_validate_planes> <PDBx:pdbx_validate_planes id="3"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>DC</PDBx:auth_comp_id> <PDBx:auth_seq_id>8</PDBx:auth_seq_id> <PDBx:rmsd>0.090</PDBx:rmsd> <PDBx:type>SIDE CHAIN</PDBx:type> </PDBx:pdbx_validate_planes> </PDBx:pdbx_validate_planesCategory> Optional identifier of the residue in which the plane is calculated This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the given angle This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue in which the plane is calculated This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Optional identifier of the residue in which the plane is calculated This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The value of the overall deviation from ideal plane for the atoms defining the plane. The type of plane - MAIN CHAIN or SIDE CHAIN atoms The value of attribute id in category pdbx_validate_planes must uniquely identify each item in the PDBX_VALIDATE_PLANES list. This is an integer serial number. Data items in the PDBX_VALIDATE_PLANES_ATOM category list the residues that contain unexpected deviations from planes centers. Example 1 <PDBx:pdbx_validate_planes_atomCategory> <PDBx:pdbx_validate_planes_atom id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.003</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>N1</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.011</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>C2</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="3"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.074</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>N2</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="4"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.005</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>N3</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="5"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.010</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>C4</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="6"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.029</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>C5</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="7"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.039</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>C6</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="8"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.074</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>O6</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="9"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.050</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>N7</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="10"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.129</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>C8</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="11"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.033</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>N9</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="12"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.147</PDBx:atom_deviation> <PDBx:auth_asym_id>DG</PDBx:auth_asym_id> <PDBx:auth_atom_id>C1&apos;</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>3</PDBx:auth_seq_id> <PDBx:plane_id>1</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> <PDBx:pdbx_validate_planes_atom id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:atom_deviation>0.069</PDBx:atom_deviation> <PDBx:auth_asym_id>DT</PDBx:auth_asym_id> <PDBx:auth_atom_id>N1</PDBx:auth_atom_id> <PDBx:auth_comp_id>A</PDBx:auth_comp_id> <PDBx:auth_seq_id>4</PDBx:auth_seq_id> <PDBx:plane_id>2</PDBx:plane_id> </PDBx:pdbx_validate_planes_atom> </PDBx:pdbx_validate_planes_atomCategory> Optional identifier of an atom site that defines the plane The model number for an atom site defining the plane This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. The deviation from the plane per atom Part of the identifier of an atom site that defines the plane This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of an atom site that defines the plane This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of an atom site that defines the plane This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of an atom site that defines the plane This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A pointer to attribute id in category pdbx_validate_planes This is an integer serial number. The value of attribute id in category pdbx_validate_planes_atom must uniquely identify each item in the PDBX_VALIDATE_PLANES_ATOM list. This is an integer serial number. Data items in the PDBX_VALIDATE_POLYMER_LINKAGE category list the polymer linkages within the entry that are outside of typlical covalent distances. Example 1 <PDBx:pdbx_validate_polymer_linkageCategory> <PDBx:pdbx_validate_polymer_linkage id="1"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id_1>B</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>B</PDBx:auth_asym_id_2> <PDBx:auth_atom_id_1 xsi:nil="true" /> <PDBx:auth_atom_id_2 xsi:nil="true" /> <PDBx:auth_comp_id_1>VAL</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>ARG</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>107</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>108</PDBx:auth_seq_id_2> <PDBx:dist>3.16</PDBx:dist> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> </PDBx:pdbx_validate_polymer_linkage> <PDBx:pdbx_validate_polymer_linkage id="2"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id_1>B</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>B</PDBx:auth_asym_id_2> <PDBx:auth_atom_id_1 xsi:nil="true" /> <PDBx:auth_atom_id_2 xsi:nil="true" /> <PDBx:auth_comp_id_1>ARG</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>LYS</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>110</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>110</PDBx:auth_seq_id_2> <PDBx:dist>2.95</PDBx:dist> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> </PDBx:pdbx_validate_polymer_linkage> </PDBx:pdbx_validate_polymer_linkageCategory> Optional identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Optional identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the given linkage Part of the identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the linkage. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the linkage. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the polymer linkage for the two atoms defined. An optional identifier of the first of the two atoms that define the linkage. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atoms that define the linkage. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The value of attribute id in category pdbx_validate_polymer_linkage must uniquely identify each item in the PDBX_VALIDATE_POLYMER_LINKAGE list. This is an integer serial number. Data items in the PDBX_VALIDATE_RMSD_ANGLE category list the covalent bond angles found in an entry that have values which deviate from expected values by more than 6*rmsd for the particular entry from the expected standard value Example 1 <PDBx:pdbx_validate_rmsd_angleCategory> <PDBx:pdbx_validate_rmsd_angle id="1"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_ins_code_3 xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:angle_deviation>-3.14</PDBx:angle_deviation> <PDBx:angle_value>117.16</PDBx:angle_value> <PDBx:auth_asym_id_1>A</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>A</PDBx:auth_asym_id_2> <PDBx:auth_asym_id_3>A</PDBx:auth_asym_id_3> <PDBx:auth_atom_id_1>NE</PDBx:auth_atom_id_1> <PDBx:auth_atom_id_2>CZ</PDBx:auth_atom_id_2> <PDBx:auth_atom_id_3>NH2</PDBx:auth_atom_id_3> <PDBx:auth_comp_id_1>ARG</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>ARG</PDBx:auth_comp_id_2> <PDBx:auth_comp_id_3>ARG</PDBx:auth_comp_id_3> <PDBx:auth_seq_id_1>35</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>35</PDBx:auth_seq_id_2> <PDBx:auth_seq_id_3>35</PDBx:auth_seq_id_3> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> <PDBx:label_alt_id_3 xsi:nil="true" /> <PDBx:linker_flag>N</PDBx:linker_flag> </PDBx:pdbx_validate_rmsd_angle> <PDBx:pdbx_validate_rmsd_angle id="2"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_ins_code_3 xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:angle_deviation>34.68</PDBx:angle_deviation> <PDBx:angle_value>148.88</PDBx:angle_value> <PDBx:auth_asym_id_1>A</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>A</PDBx:auth_asym_id_2> <PDBx:auth_asym_id_3>A</PDBx:auth_asym_id_3> <PDBx:auth_atom_id_1>CB</PDBx:auth_atom_id_1> <PDBx:auth_atom_id_2>CG</PDBx:auth_atom_id_2> <PDBx:auth_atom_id_3>CD</PDBx:auth_atom_id_3> <PDBx:auth_comp_id_1>GLU</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>GLU</PDBx:auth_comp_id_2> <PDBx:auth_comp_id_3>GLU</PDBx:auth_comp_id_3> <PDBx:auth_seq_id_1>166</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>166</PDBx:auth_seq_id_2> <PDBx:auth_seq_id_3>166</PDBx:auth_seq_id_3> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> <PDBx:label_alt_id_3 xsi:nil="true" /> <PDBx:linker_flag>N</PDBx:linker_flag> </PDBx:pdbx_validate_rmsd_angle> </PDBx:pdbx_validate_rmsd_angleCategory> Optional identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Optional identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Optional identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the given angle Value of the deviation (in degrees) from 6*REBI for the angle bounded by the three sites from the expected dictionary value. The uncertainty in the target value of the bond angle expressed as a standard deviation. The target value of the bond angle The value of the bond angle Part of the identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier of the third of the three atom sites that define the angle. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atoms that define the covalent angle. This data item is a pointer to attribute label_alt.id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atoms that define the covalent angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atoms that define the covalent angle. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A flag to indicate if the angle is between two residues The value of attribute id in category pdbx_validate_rmsd_angle must uniquely identify each item in the PDBX_VALIDATE_RMSD_ANGLE list. This is an integer serial number. Data items in the PDBX_VALIDATE_RMSD_BOND category list the covalent bonds that have values which deviate from expected values by more than 6*rmsd. Example 1 <PDBx:pdbx_validate_rmsd_bondCategory> <PDBx:pdbx_validate_rmsd_bond id="1"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id_1>A</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>A</PDBx:auth_asym_id_2> <PDBx:auth_atom_id_1>CD</PDBx:auth_atom_id_1> <PDBx:auth_atom_id_2>CE</PDBx:auth_atom_id_2> <PDBx:auth_comp_id_1>LYS</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>LYS</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>152</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>152</PDBx:auth_seq_id_2> <PDBx:bond_deviation>-0.372</PDBx:bond_deviation> <PDBx:bond_value>1.136</PDBx:bond_value> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> <PDBx:linker_flag>N</PDBx:linker_flag> </PDBx:pdbx_validate_rmsd_bond> <PDBx:pdbx_validate_rmsd_bond id="2"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>0</PDBx:PDB_model_num> <PDBx:auth_asym_id_1>A</PDBx:auth_asym_id_1> <PDBx:auth_asym_id_2>A</PDBx:auth_asym_id_2> <PDBx:auth_atom_id_1>CG</PDBx:auth_atom_id_1> <PDBx:auth_atom_id_2>CD</PDBx:auth_atom_id_2> <PDBx:auth_comp_id_1>GLU</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>GLU</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>166</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>166</PDBx:auth_seq_id_2> <PDBx:bond_deviation>-0.622</PDBx:bond_deviation> <PDBx:bond_value>0.893</PDBx:bond_value> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> <PDBx:linker_flag>N</PDBx:linker_flag> </PDBx:pdbx_validate_rmsd_bond> </PDBx:pdbx_validate_rmsd_bondCategory> Optional identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. Optional identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the given bond Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the covalent bond. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the deviation from ideal for the defined covalent bond for the two atoms defined. The uncertaintiy in target value of the bond length expressed as a standard deviation. The target value of the bond length The value of the bond length An optional identifier of the first of the two atoms that define the covalent bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atoms that define the covalent bond. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A flag to indicate if the bond is between two residues The value of attribute id in category pdbx_validate_rmsd_bond must uniquely identify each item in the PDBX_VALIDATE_RMSD_BOND list. This is an integer serial number. Data items in the PDBX_VALIDATE_SYMM_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Contacts with for symmetry related contacts are considered. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6Angstrom is used. Example 1 <PDBx:pdbx_validate_symm_contactCategory> <PDBx:pdbx_validate_symm_contact id="1"> <PDBx:PDB_ins_code_1 xsi:nil="true" /> <PDBx:PDB_ins_code_2 xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id_1 xsi:nil="true" /> <PDBx:auth_asym_id_2 xsi:nil="true" /> <PDBx:auth_atom_id_1>O</PDBx:auth_atom_id_1> <PDBx:auth_atom_id_2>O</PDBx:auth_atom_id_2> <PDBx:auth_comp_id_1>HOH</PDBx:auth_comp_id_1> <PDBx:auth_comp_id_2>HOH</PDBx:auth_comp_id_2> <PDBx:auth_seq_id_1>70</PDBx:auth_seq_id_1> <PDBx:auth_seq_id_2>70</PDBx:auth_seq_id_2> <PDBx:dist>2.05</PDBx:dist> <PDBx:label_alt_id_1 xsi:nil="true" /> <PDBx:label_alt_id_2 xsi:nil="true" /> <PDBx:site_symmetry_1>1555</PDBx:site_symmetry_1> <PDBx:site_symmetry_2>7555</PDBx:site_symmetry_2> </PDBx:pdbx_validate_symm_contact> </PDBx:pdbx_validate_symm_contactCategory> Optional identifier of the first of the two atom sites that define the close contact. Optional identifier of the second of the two atom sites that define the close contact. The model number for the given angle Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the first of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Part of the identifier of the second of the two atom sites that define the close contact. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value of the close contact for the two atoms defined. An optional identifier of the first of the two atoms that define the close contact. This data item is a pointer to attribute label_alt.id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atoms that define the close contact. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The symmetry of the first of the two atoms define the close contact. Symmetry defined in ORTEP style of 555 equal to unit cell with translations +-1 from 555 as 000 The symmetry of the second of the two atoms define the close contact. Symmetry defined in ORTEP style of 555 equal to unit cell with translations +-1 from 555 as 000 The value of attribute id in category pdbx_validate_symm_contact must uniquely identify each item in the PDBX_VALIDATE_SYMM_CONTACT list. This is an integer serial number. Data items in the PDBX_VALIDATE_TORSION category list the residues with torsion angles outside the expected ramachandran regions Example 1 <PDBx:pdbx_validate_torsionCategory> <PDBx:pdbx_validate_torsion id="1"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>SER</PDBx:auth_comp_id> <PDBx:auth_seq_id>12</PDBx:auth_seq_id> <PDBx:phi>-64.75</PDBx:phi> <PDBx:psi>2.02</PDBx:psi> </PDBx:pdbx_validate_torsion> <PDBx:pdbx_validate_torsion id="2"> <PDBx:PDB_ins_code xsi:nil="true" /> <PDBx:PDB_model_num>1</PDBx:PDB_model_num> <PDBx:auth_asym_id>A</PDBx:auth_asym_id> <PDBx:auth_comp_id>THR</PDBx:auth_comp_id> <PDBx:auth_seq_id>22</PDBx:auth_seq_id> <PDBx:phi>-116.30</PDBx:phi> <PDBx:psi>61.44</PDBx:psi> </PDBx:pdbx_validate_torsion> </PDBx:pdbx_validate_torsionCategory> Optional identifier of the residue This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. The model number for the given residue This data item is a pointer to attribute pdbx_PDB_model_num in category atom_site in the ATOM_SITE category. Part of the identifier of the residue This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. Part of the identifier of the residue This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Optional identifier of the residue This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. The Phi value that for the residue that lies outside normal limits (in combination with the Psi value) with regards to the rammachandran plot The Psi value that for the residue that lies outside normal limits (in combination with the Phi value) with regards to the rammachandran plot The value of attribute id in category pdbx_validate_torsion must uniquely identify each item in the PDBX_VALIDATE_TORSION list. This is an integer serial number. Data items in the PDBX_VERSION category record details about the version of this entry. Example 1 - <PDBx:pdbx_versionCategory> <PDBx:pdbx_version entry_id="1ABC" major_version="4" minor_version="0001" revision_type="Citation"> <PDBx:details> Primary citation page numbers added.</PDBx:details> <PDBx:revision_date>2011-05-02</PDBx:revision_date> </PDBx:pdbx_version> </PDBx:pdbx_versionCategory> A text description of any special details of the current version. Includes new 3dem experimental data items A date for the current version or revision. The date format is yyyy-mm-dd. 2006-07-12 This data item is a pointer to attribute id in category entry in the ENTRY category. Major version number for this datablock. 4 Minor version identifier for this datablock: The minor version is incremented for each datablock revision. 0004 The content type that associated with the revision. Entry title Data items in the PDBX_VIEW_CATEGORY specify the categories belonging to a category view group. An alias name for the mmCIF category may also be specified for the each category in the view. An alias name for the mmCIF category in this view. A pointer to the view_group_id in the PDBX_VIEW_CATEGORY_GROUP category. The mmCIF category identifier. Data items in the PDBX_VIEW_CATEGORY_GROUP identify collections of related mmCIF categories. Views provide a vehicle for presenting different logical arrangements of dictionary contents. A description for this collection of categories. The identifier for a collection of related mmCIF categories. Data items in the PDBX_VIEW_ITEM specify the mmCIF data items belonging to a view category. An alias name for the mmCIF item may be specified for the each item in the view category. The role of the item in the view category can be designated as mandatory, optional, or hidden. A pointer to the category_id in the PDBX_VIEW_CATEGORY category. A code to indicate if the view should permit alternatives to enumerated item values. A code to indicate the role of the data item in the view. An alias name for the mmCIF item in this view. The mmCIF item name. Data items in the PDBX_VIRTUAL_ANGLE category record details about the molecular virtual angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Example 1 - <PDBx:pdbx_virtual_angleCategory> <PDBx:pdbx_virtual_angle atom_site_id_1="1" atom_site_id_2="15" atom_site_id_3="20" model_id="1" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555"> <PDBx:value>111.6</PDBx:value> </PDBx:pdbx_virtual_angle> </PDBx:pdbx_virtual_angleCategory> An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Angle in degrees bounded by the three sites _pdbx_virtual_angle.atom_site_id_1, _pdbx_virtual_angle.atom_site_id_2 and attribute atom_site_id_3 in category pdbx_virtual_angle. The estimated standard deviation of attribute value in category pdbx_virtual_angle. The identifier of the first of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the three atom sites that define the angle specified by attribute value in category pdbx_virtual_angle. The second atom is taken to be the apex of the angle. This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the third of the three atom sites that define the angle specified by attribute value. in category pdbx_virtual_angle This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The model number for the given angle The symmetry code of the first of the three atom sites that define the angle specified by _pdbx_virtual_angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the three atom sites that define the angle specified by _pdbx_virtual_angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the third of the three atom sites that define the angle specified by _pdbx_virtual_angle. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the PDBX_VIRTUAL_BOND category record details about virtual bonds, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Example 1 - <PDBx:pdbx_virtual_bondCategory> <PDBx:pdbx_virtual_bond atom_site_id_1="1" atom_site_id_2="5" model_id="1" site_symmetry_1="1_555" site_symmetry_2="1_555"> <PDBx:dist>3.40</PDBx:dist> </PDBx:pdbx_virtual_bond> </PDBx:pdbx_virtual_bondCategory> An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The intramolecular bond distance in angstroms. The estimated standard deviation of attribute dist in category pdbx_virtual_bond. The identifier of the first of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the two atom sites that define the bond specified by attribute dist. in category pdbx_virtual_bond This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The model number for the given bond The symmetry code of the first of the two atom sites that define the bond specified by attribute dist in category pdbx_virtual_bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the two atom sites that define the bond specified by attribute dist in category pdbx_virtual_bond. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the PDBX_VIRTUAL_TORSION category record details about virtual torsion angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data. Example 1 - <PDBx:pdbx_virtual_torsionCategory> <PDBx:pdbx_virtual_torsion atom_site_id_1="1" atom_site_id_2="2" atom_site_id_3="5" atom_site_id_4="9" model_id="1" site_symmetry_1="1_555" site_symmetry_2="1_555" site_symmetry_3="1_555" site_symmetry_4="1_555"> <PDBx:value>71.8</PDBx:value> </PDBx:pdbx_virtual_torsion> </PDBx:pdbx_virtual_torsionCategory> An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. An optional identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. An optional identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The value of the torsion angle in degrees. The estimated standard deviation of attribute value in category pdbx_virtual_torsion. The identifier of the first of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the second of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the third of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The identifier of the fourth of the four atom sites that define the torsion angle specified by attribute value. in category pdbx_virtual_torsion This data item is a pointer to attribute id in category atom_site in the ATOM_SITE category. The model number for the given angle The symmetry code of the first of the four atom sites that define the torsion angle specified by attribute value in category pdbx_virtual_torsion. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the second of the four atom sites that define the torsion angle specified by attribute value in category pdbx_virtual_torsion. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the third of the four atom sites that define the torsion angle specified by attribute value in category pdbx_virtual_torsion. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The symmetry code of the fourth of the four atom sites that define the torsion angle specified by attribute value in category pdbx_virtual_torsion. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Parameter and topology files used in X-PLOR/CNS refinement. <PDBx:pdbx_xplor_fileCategory> <PDBx:pdbx_xplor_file pdbx_refine_id="x-ray" serial_no="1"> <PDBx:param_file>parm_hol.dat</PDBx:param_file> <PDBx:topol_file>topol_hol.dat</PDBx:topol_file> </PDBx:pdbx_xplor_file> </PDBx:pdbx_xplor_fileCategory> Parameter file name in X-PLOR/CNS refinement. PARAM_NDBX_HIGH.DNA Topology file name in X-PLOR/CNS refinement. TOP_NDBX.DNA This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category pdbx_xplor_file can be used to distinguish the results of joint refinements. Serial number. Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. Details about the application of each method are listed in the appropriate subcategories. Example 1 - hypothetical example. <PDBx:phasingCategory> <PDBx:phasing method="mir"></PDBx:phasing> <PDBx:phasing method="averaging"></PDBx:phasing> </PDBx:phasingCategory> A listing of the method or methods used to phase this structure. phasing by ab initio methods abinitio phase improvement by averaging over multiple images of the structure averaging phasing by direct methods dm phasing by iterative single-wavelength anomalous scattering isas phasing by iterative single-wavelength isomorphous replacement isir phasing beginning with phases calculated from an isomorphous structure isomorphous phasing by multiple-wavelength anomalous dispersion mad phasing by multiple isomorphous replacement mir phasing by multiple isomorphous replacement with anomalous scattering miras phasing by molecular replacement mr phasing by single isomorphous replacement sir phasing by single isomorphous replacement with anomalous scattering siras Data items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <PDBx:phasing_MADCategory> <PDBx:phasing_MAD entry_id="NCAD"></PDBx:phasing_MAD> </PDBx:phasing_MADCategory> A description of special aspects of the MAD phasing. A description of the MAD phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MAD phasing program. attribute pdbx_R_cullis in category phasing_MAD records R_cullis for MAD phasing. attribute pdbx_R_cullis_acentric in category phasing_MAD records R_cullis using acentric data for MAD phasing. attribute pdbx_R_cullis_centric in category phasing_MAD records R_cullis using centric data for MAD phasing. attribute pdbx_R_kraut in category phasing_MAD records R_kraut for MAD phasing. attribute pdbx_R_kraut_acentric in category phasing_MAD records R_kraut using acentric data for MAD phasing. attribute pdbx_R_kraut_centric in category phasing_MAD records R_kraut using centric data for MAD phasing. attribute pdbx_anom_scat_method in category phasing_MAD records the method used to locate anomalous scatterers for MAD phasing. attribute pdbx_d_res_high in category phasing_MAD records the highest resolution for MAD phasing. attribute pdbx_d_res_low in category phasing_MAD records the lowest resolution for MAD phasing. attribute pdbx_fom in category phasing_MAD records the figure of merit for MAD phasing. attribute pdbx_fom_acentric in category phasing_MAD records the figure of merit using acentric data for MAD phasing. attribute pdbx_fom_centric in category phasing_MAD records the figure of merit using centric data for MAD phasing. attribute pdbx_loc in category phasing_MAD records lack of closure for MAD phasing. attribute pdbx_loc_acentric in category phasing_MAD records lack of closure using acentric data for MAD phasing. attribute pdbx_loc_centric in category phasing_MAD records lack of closure using centric data for MAD phasing. attribute pdbx_loc in category phasing_MAD records the number of data sets used for MAD phasing. attribute pdbx_power in category phasing_MAD records phasing power for MAD phasing. attribute pdbx_power_acentric in category phasing_MAD records phasing power using acentric data for MAD phasing. attribute pdbx_power_centric in category phasing_MAD records phasing power using centric data for MAD phasing. attribute pdbx_reflns in category phasing_MAD records the number of reflections used for MAD phasing. attribute pdbx_reflns_acentric in category phasing_MAD records the number of acentric reflections for MAD phasing. attribute pdbx_reflns_centric in category phasing_MAD records the number of centric reflections for MAD phasing. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <PDBx:phasing_MAD_clustCategory> <PDBx:phasing_MAD_clust expt_id="1" id="4 wavelength"> <PDBx:number_set>4</PDBx:number_set> </PDBx:phasing_MAD_clust> <PDBx:phasing_MAD_clust expt_id="1" id="5 wavelength"> <PDBx:number_set>5</PDBx:number_set> </PDBx:phasing_MAD_clust> <PDBx:phasing_MAD_clust expt_id="2" id="5 wavelength"> <PDBx:number_set>5</PDBx:number_set> </PDBx:phasing_MAD_clust> </PDBx:phasing_MAD_clustCategory> The number of data sets in this cluster of data sets. This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. The value of attribute id in category phasing_MAD_clust must, together with attribute expt_id in category phasing_MAD_clust, uniquely identify a record in the PHASING_MAD_CLUST list. Note that this item need not be a number; it can be any unique identifier. Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <PDBx:phasing_MAD_exptCategory> <PDBx:phasing_MAD_expt id="1"> <PDBx:R_normal_all>0.063</PDBx:R_normal_all> <PDBx:R_normal_anom_scat>0.451</PDBx:R_normal_anom_scat> <PDBx:delta_delta_phi>58.5</PDBx:delta_delta_phi> <PDBx:delta_phi_sigma>20.3</PDBx:delta_phi_sigma> <PDBx:mean_fom>0.88</PDBx:mean_fom> <PDBx:number_clust>2</PDBx:number_clust> </PDBx:phasing_MAD_expt> <PDBx:phasing_MAD_expt id="2"> <PDBx:R_normal_all>0.051</PDBx:R_normal_all> <PDBx:R_normal_anom_scat>0.419</PDBx:R_normal_anom_scat> <PDBx:delta_delta_phi>36.8</PDBx:delta_delta_phi> <PDBx:delta_phi_sigma>18.2</PDBx:delta_phi_sigma> <PDBx:mean_fom>0.93</PDBx:mean_fom> <PDBx:number_clust>1</PDBx:number_clust> </PDBx:phasing_MAD_expt> </PDBx:phasing_MAD_exptCategory> Definition... Definition... The difference between two independent determinations of attribute delta_phi in category phasing_MAD_expt. The phase difference between F~t~(h), the structure factor due to normal scattering from all atoms, and F~a~(h), the structure factor due to normal scattering from only the anomalous scatterers. The standard uncertainty (estimated standard deviation) of attribute delta_phi in category phasing_MAD_expt. The mean figure of merit. The number of clusters of data sets in this phasing experiment. The value of attribute id in category phasing_MAD_expt must uniquely identify each record in the PHASING_MAD_EXPT list. Data items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <PDBx:phasing_MAD_ratioCategory> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.4013"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.084</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.076</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3857"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3852"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.051</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3847"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.044</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.110</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.049</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.049</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.149</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.072</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.039</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.102</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.071</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.4013"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.114</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.111</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3857"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.089</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3852"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.086</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.4013" wavelength_2="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.077</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.140</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.127</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.089</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.155</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.119</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.082</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="4 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.124</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.120</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.075</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.027</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.041</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.060</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3784"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.057</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.2862"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.072</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.105</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.032</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.036</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3784"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.044</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.2862"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.065</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.072</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.031</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3784"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.040</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.2862"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.3784"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.059</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.032</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.2862"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.2862" wavelength_2="1.3847"> <PDBx:d_res_high>4.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.058</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.028</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3857"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.078</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.075</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3852"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.059</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.067</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.3784"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.084</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3857" wavelength_2="1.2862"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.073</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3852"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.101</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.088</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.066</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.3784"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.082</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3852" wavelength_2="1.2862"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.097</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.074</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.3784"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.081</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3847" wavelength_2="1.2862"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.085</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.3784"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.114</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.089</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.3784" wavelength_2="1.2862"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.103</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="1" wavelength_1="1.2862" wavelength_2="1.2862"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>4.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.062</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.060</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7263"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.035</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7251"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.028</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7284"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.023</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7246"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.025</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7217"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.026</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7251"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7284"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.029</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7246"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.031</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7217"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.035</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7284"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.075</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.030</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7246"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.023</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7217"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.027</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7246"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.069</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.026</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7217"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.024</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7217" wavelength_2="0.7284"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.028</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7263"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.060</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.050</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7251"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.056</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7284"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.055</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7246"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.053</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7263" wavelength_2="0.7217"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.056</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7251"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.089</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.050</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7284"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.054</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7246"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.058</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7251" wavelength_2="0.7217"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.063</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7284"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.104</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.057</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7246"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.052</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7284" wavelength_2="0.7217"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.057</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7246"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.098</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.052</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7246" wavelength_2="0.7217"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl xsi:nil="true" /> <PDBx:ratio_one_wl_centric xsi:nil="true" /> <PDBx:ratio_two_wl>0.054</PDBx:ratio_two_wl> </PDBx:phasing_MAD_ratio> <PDBx:phasing_MAD_ratio clust_id="5 wavelength" expt_id="2" wavelength_1="0.7217" wavelength_2="0.7284"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>3.00</PDBx:d_res_low> <PDBx:ratio_one_wl>0.089</PDBx:ratio_one_wl> <PDBx:ratio_one_wl_centric>0.060</PDBx:ratio_one_wl_centric> <PDBx:ratio_two_wl xsi:nil="true" /> </PDBx:phasing_MAD_ratio> </PDBx:phasing_MAD_ratioCategory> The lowest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the highest resolution. The highest value for the interplanar spacings for the reflection data used for the comparison of Bijvoet differences. This is called the lowest resolution. The root-mean-square Bijvoet difference at one wavelength for all reflections. The root-mean-square Bijvoet difference at one wavelength for centric reflections. This would be equal to zero for perfect data and thus serves as an estimate of the noise in the anomalous signals. The root-mean-square dispersive Bijvoet difference between two wavelengths for all reflections. This data item is a pointer to attribute id in category phasing_MAD_clust in the PHASING_MAD_CLUST category. This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. This data item is a pointer to attribute wavelength in category phasing_MAD_set in the PHASING_MAD_SET category. This data item is a pointer to attribute wavelength in category phasing_MAD_set in the PHASING_MAD_SET category. Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment. Example 1 - based on a paper by Shapiro et al. [Nature (London) (1995), 374, 327-337]. <PDBx:phasing_MAD_setCategory> <PDBx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="aa" wavelength="1.4013"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>3.80</PDBx:f_double_prime> <PDBx:f_prime>-12.48</PDBx:f_prime> <PDBx:wavelength_details>pre-edge</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="bb" wavelength="1.3857"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>17.20</PDBx:f_double_prime> <PDBx:f_prime>-31.22</PDBx:f_prime> <PDBx:wavelength_details>peak</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="cc" wavelength="1.3852"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>29.17</PDBx:f_double_prime> <PDBx:f_prime>-13.97</PDBx:f_prime> <PDBx:wavelength_details>edge</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="4 wavelength" expt_id="1" set_id="dd" wavelength="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>17.34</PDBx:f_double_prime> <PDBx:f_prime>-6.67</PDBx:f_prime> <PDBx:wavelength_details>remote</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ee" wavelength="1.3857"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>14.84</PDBx:f_double_prime> <PDBx:f_prime>-28.33</PDBx:f_prime> <PDBx:wavelength_details>ascending edge</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ff" wavelength="1.3852"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>30.23</PDBx:f_double_prime> <PDBx:f_prime>-21.50</PDBx:f_prime> <PDBx:wavelength_details>peak</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="gg" wavelength="1.3847"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>20.35</PDBx:f_double_prime> <PDBx:f_prime>-10.71</PDBx:f_prime> <PDBx:wavelength_details>descending edge</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="hh" wavelength="1.3784"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>11.84</PDBx:f_double_prime> <PDBx:f_prime>-14.45</PDBx:f_prime> <PDBx:wavelength_details>remote 1</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="1" set_id="ii" wavelength="1.2862"> <PDBx:d_res_high>3.00</PDBx:d_res_high> <PDBx:d_res_low>20.00</PDBx:d_res_low> <PDBx:f_double_prime>9.01</PDBx:f_double_prime> <PDBx:f_prime>-9.03</PDBx:f_prime> <PDBx:wavelength_details>remote 2</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="jj" wavelength="0.7263"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:f_double_prime>4.08</PDBx:f_double_prime> <PDBx:f_prime>-21.10</PDBx:f_prime> <PDBx:wavelength_details>pre-edge</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="kk" wavelength="0.7251"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:f_double_prime>7.92</PDBx:f_double_prime> <PDBx:f_prime>-34.72</PDBx:f_prime> <PDBx:wavelength_details>edge</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="ll" wavelength="0.7248"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:f_double_prime>10.30</PDBx:f_double_prime> <PDBx:f_prime>-24.87</PDBx:f_prime> <PDBx:wavelength_details>peak</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="mm" wavelength="0.7246"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:f_double_prime>9.62</PDBx:f_double_prime> <PDBx:f_prime>-17.43</PDBx:f_prime> <PDBx:wavelength_details>descending edge</PDBx:wavelength_details> </PDBx:phasing_MAD_set> <PDBx:phasing_MAD_set clust_id="5 wavelength" expt_id="2" set_id="nn" wavelength="0.7217"> <PDBx:d_res_high>1.90</PDBx:d_res_high> <PDBx:d_res_low>15.00</PDBx:d_res_low> <PDBx:f_double_prime>8.40</PDBx:f_double_prime> <PDBx:f_prime>-13.26</PDBx:f_prime> <PDBx:wavelength_details>remote</PDBx:wavelength_details> </PDBx:phasing_MAD_set> </PDBx:phasing_MAD_setCategory> The lowest value for the interplanar spacings for the reflection data used for this set of data. This is called the highest resolution. The highest value for the interplanar spacings for the reflection data used for this set of data. This is called the lowest resolution. The f'' component of the anomalous scattering factor for this wavelength. The f' component of the anomalous scattering factor for this wavelength. record the type of heavy atoms which produce anomolous singal. record the refined f_double_prime (not from experiment). record the refined f_prime (not from experiment). A descriptor for this wavelength in this cluster of data sets. peak remote ascending edge This data item is a pointer to attribute id in category phasing_MAD_clust in the PHASING_MAD_CLUST category. This data item is a pointer to attribute id in category phasing_MAD_expt in the PHASING_MAD_EXPT category. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. The wavelength at which this data set was measured. Data items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved. All isomorphous-replacement-based techniques are covered by this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR) and single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS). Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. <PDBx:phasing_MIRCategory> <PDBx:phasing_MIR entry_id="1ABC"> <PDBx:method> Standard phase refinement (Blow &amp; Crick, 1959)</PDBx:method> </PDBx:phasing_MIR> </PDBx:phasing_MIRCategory> The mean value of the figure of merit m for all reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. The mean value of the figure of merit m for the acentric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. The mean value of the figure of merit m for the centric reflections phased in the native data set. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. The lowest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the highest resolution. The highest value in angstroms for the interplanar spacings for the reflection data used for the native data set. This is called the lowest resolution. A description of special aspects of the isomorphous-replacement phasing. A description of the MIR phasing method applied to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the MIR phasing program. The number of derivatives used in this phasing experiment. The total number of reflections phased in the native data set. The number of acentric reflections phased in the native data set. The number of centric reflections phased in the native data set. Criterion used to limit the reflections used in the phasing calculations. > 4 \s(I) This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via attribute der_set_id in category phasing_MIR_der and attribute native_set_id in category phasing_MIR_der. Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738]. <PDBx:phasing_MIR_derCategory> <PDBx:phasing_MIR_der id="KAu(CN)2"> <PDBx:details>major site interpreted in difference Patterson</PDBx:details> <PDBx:number_of_sites>3</PDBx:number_of_sites> </PDBx:phasing_MIR_der> <PDBx:phasing_MIR_der id="K2HgI4"> <PDBx:details>sites found in cross-difference Fourier</PDBx:details> <PDBx:number_of_sites>6</PDBx:number_of_sites> </PDBx:phasing_MIR_der> <PDBx:phasing_MIR_der id="K3IrCl6"> <PDBx:details>sites found in cross-difference Fourier</PDBx:details> <PDBx:number_of_sites>2</PDBx:number_of_sites> </PDBx:phasing_MIR_der> <PDBx:phasing_MIR_der id="All"> <PDBx:details>data for all three derivatives combined</PDBx:details> <PDBx:number_of_sites>11</PDBx:number_of_sites> </PDBx:phasing_MIR_der> </PDBx:phasing_MIR_derCategory> Residual factor R~cullis,acen~ for acentric reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for acentric reflections, which is how it is used in this data item. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis,acen~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. Residual factor R~cullis,ano~ for anomalous reflections for this derivative. The Cullis R factor was originally defined only for centric reflections. It is, however, also a useful statistical measure for anomalous reflections, which is how it is used in this data item. This is tabulated for acentric terms. A value less than 1.0 means there is some contribution to the phasing from the anomalous data. sum |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~| R~cullis,ano~ = ------------------------------------------------ sum|Fph+~obs~ - Fph-~obs~| Fph+~obs~ = the observed positive Friedel structure-factor amplitude for the derivative Fph-~obs~ = the observed negative Friedel structure-factor amplitude for the derivative Fh+~calc~ = the calculated positive Friedel structure-factor amplitude from the heavy-atom model Fh-~calc~ = the calculated negative Friedel structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. Residual factor R~cullis~ for centric reflections for this derivative. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. The lowest value for the interplanar spacings for the reflection data used for this derivative. This is called the highest resolution. The highest value for the interplanar spacings for the reflection data used for this derivative. This is called the lowest resolution. The data set that was treated as the derivative in this experiment. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. A description of special aspects of this derivative, its data, its solution or its use in phasing. The data set that was treated as the native in this experiment. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. The number of heavy-atom sites in this derivative. record R_cullis for each derivative. record R_kraut obtained from all data data for each derivative. record R_kraut obtained from acentric data for each derivative. record R_kraut obtained from centric data for each derivative. record figure of merit obtained from all data for each derivative. record figure of merit obtained from acentric data for each derivative. record figure of merit obtained from centric data for each derivative. record lack of closure obtained from all data for each derivative. record lack of closure obtained from acentric data for each derivative. record lack of closure obtained from centric data for each derivative. record phasing power for each derivative. record number of reflections used for each derivative. The mean phasing power P for acentric reflections for this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of this derivative Fph~calc~ = the calculated structure-factor amplitude of this derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections The mean phasing power P for centric reflections for this derivative. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections The number of acentric reflections used in phasing for this derivative. The number of anomalous reflections used in phasing for this derivative. The number of centric reflections used in phasing for this derivative. Criteria used to limit the reflections used in the phasing calculations. > 4 \s(I) The value of attribute id in category phasing_MIR_der must uniquely identify a record in the PHASING_MIR_DER list. Note that this item need not be a number; it can be any unique identifier. KAu(CN)2 K2HgI4_anom K2HgI4_iso Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_refln indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will be given in the PHASING_SET_REFLN category. However, these items can also be listed here for completeness. Example 1 - based on laboratory records for the 6,1,25 reflection of an Hg/Pt derivative of protein NS1. <PDBx:phasing_MIR_der_reflnCategory> <PDBx:phasing_MIR_der_refln der_id="HGPT1" index_h="6" index_k="1" index_l="25" set_id="NS1-96"> <PDBx:F_calc_au>106.66</PDBx:F_calc_au> <PDBx:F_meas_au>204.67</PDBx:F_meas_au> <PDBx:F_meas_sigma>6.21</PDBx:F_meas_sigma> <PDBx:HL_A_iso>-3.15</PDBx:HL_A_iso> <PDBx:HL_B_iso>-0.76</PDBx:HL_B_iso> <PDBx:HL_C_iso>0.65</PDBx:HL_C_iso> <PDBx:HL_D_iso>0.23</PDBx:HL_D_iso> <PDBx:phase_calc>194.48</PDBx:phase_calc> </PDBx:phasing_MIR_der_refln> </PDBx:phasing_MIR_der_reflnCategory> The calculated value of the structure factor for this derivative, in electrons. The calculated value of the structure factor for this derivative, in arbitrary units. The measured value of the structure factor for this derivative, in electrons. The measured value of the structure factor for this derivative, in arbitrary units. The standard uncertainty (estimated standard deviation) of attribute F_meas in category phasing_MIR_der_refln, in electrons. The standard uncertainty (estimated standard deviation) of attribute F_meas_au in category phasing_MIR_der_refln, in arbitrary units. The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * cos(alphah~calc~) A~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the calculated phase from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection for this derivative. -2.0 * (Fp~obs~^2^ + Fh~calc~^2^ - Fph~obs~^2^) * Fp~obs~ * sin(alphah~calc~) B~iso~ = ----------------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection for this derivative. -Fp~obs~^2^ * [sin(alphah~calc~)^2^ - cos(alphah~calc~)^2^] C~iso~ = ------------------------------------ E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection for this derivative. -2.0 * Fp~obs~^2^ * sin(alphah~calc~)^2^ * cos(alphah~calc~)^2^ D~iso~ = ---------------------------------------- E^2^ E = (Fph~obs~ - Fp~obs~ - Fh~calc~)^2^ for centric reflections = [(Fph~obs~ - Fp~obs~) * 2^1/2^ - Fh~calc~]^2^ for acentric reflections Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model alphah~calc~ = the phase calculated from the heavy-atom model This coefficient appears in the expression for the phase probability of each isomorphous derivative: P~i~(alpha) = exp[k + A * cos(alpha) + B * sin(alpha) + C * cos(2 * alpha) + D * sin(2 * alpha)] Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. The calculated value of the structure-factor phase based on the heavy-atom model for this derivative in degrees. This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. Miller index h for this reflection for this derivative. Miller index k for this reflection for this derivative. Miller index l for this reflection for this derivative. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. Data items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_shell indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. <PDBx:phasing_MIR_der_shellCategory> <PDBx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="KAu(CN)2"> <PDBx:ha_ampl>54</PDBx:ha_ampl> <PDBx:loc>26</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="KAu(CN)2"> <PDBx:ha_ampl>54</PDBx:ha_ampl> <PDBx:loc>20</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="KAu(CN)2"> <PDBx:ha_ampl>50</PDBx:ha_ampl> <PDBx:loc>20</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="KAu(CN)2"> <PDBx:ha_ampl>44</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="KAu(CN)2"> <PDBx:ha_ampl>39</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="KAu(CN)2"> <PDBx:ha_ampl>33</PDBx:ha_ampl> <PDBx:loc>21</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="KAu(CN)2"> <PDBx:ha_ampl>28</PDBx:ha_ampl> <PDBx:loc>17</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="KAu(CN)2"> <PDBx:ha_ampl>38</PDBx:ha_ampl> <PDBx:loc>21</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="K2HgI4"> <PDBx:ha_ampl>149</PDBx:ha_ampl> <PDBx:loc>87</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="K2HgI4"> <PDBx:ha_ampl>121</PDBx:ha_ampl> <PDBx:loc>73</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="K2HgI4"> <PDBx:ha_ampl>95</PDBx:ha_ampl> <PDBx:loc>61</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="K2HgI4"> <PDBx:ha_ampl>80</PDBx:ha_ampl> <PDBx:loc>60</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="K2HgI4"> <PDBx:ha_ampl>73</PDBx:ha_ampl> <PDBx:loc>63</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="K2HgI4"> <PDBx:ha_ampl>68</PDBx:ha_ampl> <PDBx:loc>57</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="K2HgI4"> <PDBx:ha_ampl>63</PDBx:ha_ampl> <PDBx:loc>46</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="K2HgI4"> <PDBx:ha_ampl>79</PDBx:ha_ampl> <PDBx:loc>58</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="8.3" d_res_low="15.0" der_id="K3IrCl6"> <PDBx:ha_ampl>33</PDBx:ha_ampl> <PDBx:loc>27</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="6.4" d_res_low="8.3" der_id="K3IrCl6"> <PDBx:ha_ampl>40</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="5.2" d_res_low="6.4" der_id="K3IrCl6"> <PDBx:ha_ampl>31</PDBx:ha_ampl> <PDBx:loc>22</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="4.4" d_res_low="5.2" der_id="K3IrCl6"> <PDBx:ha_ampl>27</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.8" d_res_low="4.4" der_id="K3IrCl6"> <PDBx:ha_ampl>22</PDBx:ha_ampl> <PDBx:loc>23</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.4" d_res_low="3.8" der_id="K3IrCl6"> <PDBx:ha_ampl>19</PDBx:ha_ampl> <PDBx:loc>20</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="3.4" der_id="K3IrCl6"> <PDBx:ha_ampl>16</PDBx:ha_ampl> <PDBx:loc>20</PDBx:loc> </PDBx:phasing_MIR_der_shell> <PDBx:phasing_MIR_der_shell d_res_high="3.0" d_res_low="15.0" der_id="K3IrCl6"> <PDBx:ha_ampl>23</PDBx:ha_ampl> <PDBx:loc>21</PDBx:loc> </PDBx:phasing_MIR_der_shell> </PDBx:phasing_MIR_der_shellCategory> Residual factor R~cullis~ for centric reflections for this derivative in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. Residual factor R~kraut~ for general reflections for this derivative in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424. The mean value of the figure of merit m for reflections for this derivative in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that the phase angle alpha is correct int is taken over the range alpha = 0 to 2 pi. The mean heavy-atom amplitude for reflections for this derivative in this shell. The mean lack-of-closure error loc for reflections for this derivative in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections record R Cullis obtained from acentric data for each derivative, but broken into resolution shells record R Cullis obtained from centric data for each derivative, but broken into resolution shells record R Kraut obtained from acentric data for each derivative, but broken into resolution shells record R Kraut obtained from centric data for each derivative, but broken into resolution shells record figure of merit obtained from acentric data for each derivative, but broken into resolution shells record figure of merit obtained from centric data for each derivative, but broken into resolution shells record lack of closure obtained from acentric data for each derivative, but broken into resolution shells record lack of closure obtained from centric data for each derivative, but broken into resolution shells record phasing power obtained from acentric data for each derivative, but broken into resolution shells record phasing power obtained from centric data for each derivative, but broken into resolution shells record number of acentric reflections used for phasing for each derivative, but broken into resolution shells record number of centric reflections used for phasing for each derivative, but broken into resolution shells The mean of the phase values for reflections for this derivative in this shell. The mean phasing power P for reflections for this derivative in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections The number of reflections in this shell. The lowest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the highest resolution. The highest value for the interplanar spacings for the reflection data for this derivative in this shell. This is called the lowest resolution. This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. Data items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment. This list may contain information from a number of different derivatives; attribute der_id in category phasing_MIR_der_site indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with occupancies converted from electrons to fractional. <PDBx:phasing_MIR_der_siteCategory> <PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="1"> <PDBx:B_iso>33.0</PDBx:B_iso> <PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol> <PDBx:fract_x>0.082</PDBx:fract_x> <PDBx:fract_y>0.266</PDBx:fract_y> <PDBx:fract_z>0.615</PDBx:fract_z> <PDBx:occupancy>0.40</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="2"> <PDBx:B_iso>25.9</PDBx:B_iso> <PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol> <PDBx:fract_x>0.607</PDBx:fract_x> <PDBx:fract_y>0.217</PDBx:fract_y> <PDBx:fract_z>0.816</PDBx:fract_z> <PDBx:occupancy>0.03</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="KAu(CN)2" id="3"> <PDBx:B_iso>15.7</PDBx:B_iso> <PDBx:atom_type_symbol>Au</PDBx:atom_type_symbol> <PDBx:fract_x>0.263</PDBx:fract_x> <PDBx:fract_y>0.782</PDBx:fract_y> <PDBx:fract_z>0.906</PDBx:fract_z> <PDBx:occupancy>0.02</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="1"> <PDBx:B_iso>33.7</PDBx:B_iso> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:fract_x>0.048</PDBx:fract_x> <PDBx:fract_y>0.286</PDBx:fract_y> <PDBx:fract_z>0.636</PDBx:fract_z> <PDBx:occupancy>0.63</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="2"> <PDBx:B_iso>36.7</PDBx:B_iso> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:fract_x>0.913</PDBx:fract_x> <PDBx:fract_y>0.768</PDBx:fract_y> <PDBx:fract_z>0.889</PDBx:fract_z> <PDBx:occupancy>0.34</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="3"> <PDBx:B_iso>24.2</PDBx:B_iso> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:fract_x>0.974</PDBx:fract_x> <PDBx:fract_y>0.455</PDBx:fract_y> <PDBx:fract_z>0.974</PDBx:fract_z> <PDBx:occupancy>0.23</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="4"> <PDBx:B_iso>14.7</PDBx:B_iso> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:fract_x>0.903</PDBx:fract_x> <PDBx:fract_y>0.836</PDBx:fract_y> <PDBx:fract_z>0.859</PDBx:fract_z> <PDBx:occupancy>0.28</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="5"> <PDBx:B_iso>6.4</PDBx:B_iso> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:fract_x>0.489</PDBx:fract_x> <PDBx:fract_y>0.200</PDBx:fract_y> <PDBx:fract_z>0.885</PDBx:fract_z> <PDBx:occupancy>0.07</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K2HgI4" id="6"> <PDBx:B_iso>32.9</PDBx:B_iso> <PDBx:atom_type_symbol>Hg</PDBx:atom_type_symbol> <PDBx:fract_x>0.162</PDBx:fract_x> <PDBx:fract_y>0.799</PDBx:fract_y> <PDBx:fract_z>0.889</PDBx:fract_z> <PDBx:occupancy>0.07</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K3IrCl6" id="1"> <PDBx:B_iso>40.8</PDBx:B_iso> <PDBx:atom_type_symbol>Ir</PDBx:atom_type_symbol> <PDBx:fract_x>0.209</PDBx:fract_x> <PDBx:fract_y>0.739</PDBx:fract_y> <PDBx:fract_z>0.758</PDBx:fract_z> <PDBx:occupancy>0.26</PDBx:occupancy> </PDBx:phasing_MIR_der_site> <PDBx:phasing_MIR_der_site der_id="K3IrCl6" id="2"> <PDBx:B_iso>24.9</PDBx:B_iso> <PDBx:atom_type_symbol>Ir</PDBx:atom_type_symbol> <PDBx:fract_x>0.279</PDBx:fract_x> <PDBx:fract_y>0.613</PDBx:fract_y> <PDBx:fract_z>0.752</PDBx:fract_z> <PDBx:occupancy>0.05</PDBx:occupancy> </PDBx:phasing_MIR_der_site> </PDBx:phasing_MIR_der_siteCategory> Isotropic displacement parameter for this heavy-atom site in this derivative. The standard uncertainty (estimated standard deviation) of attribute B_iso in category phasing_MIR_der_site. The x coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The standard uncertainty (estimated standard deviation) of attribute Cartn_x in category phasing_MIR_der_site. The y coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The standard uncertainty (estimated standard deviation) of attribute Cartn_y in category phasing_MIR_der_site. The z coordinate of this heavy-atom position in this derivative specified as orthogonal angstroms. The orthogonal Cartesian axes are related to the cell axes as specified by the description given in attribute Cartn_transform_axes in category atom_sites. The standard uncertainty (estimated standard deviation) of attribute Cartn_z in category phasing_MIR_der_site. This data item is a pointer to attribute symbol in category atom_type in the ATOM_TYPE category. The scattering factors referenced via this data item should be those used in the refinement of the heavy-atom data; in some cases this is the scattering factor for the single heavy atom, in other cases these are the scattering factors for an atomic cluster. A description of special aspects of the derivative site. binds to His 117 minor site obtained from difference Fourier same as site 2 in the K2HgI4 derivative The x coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_a in category cell. The standard uncertainty (estimated standard deviation) of attribute fract_x in category phasing_MIR_der_site. The y coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_b in category cell. The standard uncertainty (estimated standard deviation) of attribute fract_y in category phasing_MIR_der_site. The z coordinate of this heavy-atom position in this derivative specified as a fraction of attribute length_c in category cell. The standard uncertainty (estimated standard deviation) of attribute fract_z in category phasing_MIR_der_site. The fraction of the atom type present at this heavy-atom site in a given derivative. The sum of the occupancies of all the atom types at this site may not significantly exceed 1.0 unless it is a dummy site. The relative anomalous occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. The standard uncertainty (estimated standard deviation) of attribute occupancy_anom in category phasing_MIR_der_site. The relative real isotropic occupancy of the atom type present at this heavy-atom site in a given derivative. This atom occupancy will probably be on an arbitrary scale. The standard uncertainty (estimated standard deviation) of attribute occupancy_iso in category phasing_MIR_der_site. This data item is a pointer to attribute id in category phasing_MIR_der in the PHASING_MIR_DER category. The value of attribute id in category phasing_MIR_der_site must uniquely identify each site in each derivative in the PHASING_MIR_DER_SITE list. The atom identifiers need not be unique over all sites in all derivatives; they need only be unique for each site in each derivative. Note that this item need not be a number; it can be any unique identifier. Data items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution. Example 1 - based on a paper by Zanotti et al. [J. Biol. Chem. (1993), 268, 10728-10738] with addition of an arbitrary low-resolution limit. <PDBx:phasing_MIR_shellCategory> <PDBx:phasing_MIR_shell d_res_high="8.3" d_res_low="15.0"> <PDBx:FOM>0.69</PDBx:FOM> <PDBx:reflns>80</PDBx:reflns> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_high="6.4" d_res_low="8.3"> <PDBx:FOM>0.73</PDBx:FOM> <PDBx:reflns>184</PDBx:reflns> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_high="5.2" d_res_low="6.4"> <PDBx:FOM>0.72</PDBx:FOM> <PDBx:reflns>288</PDBx:reflns> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_high="4.4" d_res_low="5.2"> <PDBx:FOM>0.65</PDBx:FOM> <PDBx:reflns>406</PDBx:reflns> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_high="3.8" d_res_low="4.4"> <PDBx:FOM>0.54</PDBx:FOM> <PDBx:reflns>554</PDBx:reflns> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_high="3.4" d_res_low="3.8"> <PDBx:FOM>0.53</PDBx:FOM> <PDBx:reflns>730</PDBx:reflns> </PDBx:phasing_MIR_shell> <PDBx:phasing_MIR_shell d_res_high="3.0" d_res_low="3.4"> <PDBx:FOM>0.50</PDBx:FOM> <PDBx:reflns>939</PDBx:reflns> </PDBx:phasing_MIR_shell> </PDBx:phasing_MIR_shellCategory> The mean value of the figure of merit m for reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~alpha~ = the probability that the phase angle alpha is correct the integral is taken over the range alpha = 0 to 2 pi. The mean value of the figure of merit m for acentric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. The mean value of the figure of merit m for centric reflections in this shell. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct the integral is taken over the range alpha = 0 to 2 pi. Residual factor R~cullis~ for centric reflections in this shell. sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ | R~cullis~ = ---------------------------------------- sum|Fph~obs~ - Fp~obs~| Fp~obs~ = the observed structure-factor amplitude of the native Fph~obs~ = the observed structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G. & North, A. C. T. (1961). Proc. R. Soc. London Ser. A, 265, 15-38. Residual factor R~kraut~ for general reflections in this shell. sum|Fph~obs~ - Fph~calc~| R~kraut~ = ------------------------- sum|Fph~obs~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections Ref: Kraut, J., Sieker, L. C., High, D. F. & Freer, S. T. (1962). Proc. Natl Acad. Sci. USA, 48, 1417-1424. The mean lack-of-closure error loc for reflections in this shell. loc = sum|Fph~obs~ - Fph~calc~| Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative sum is taken over the specified reflections The mean of the phase values for all reflections in this shell. record R_Cullis from from acentric reflection for each shell. record R_Cullis from from centric reflection for each shell. record R_kraut from from acentric reflection for each shell. record R_Kraut from from centric reflection for each shell. record lack of closure from acentric reflection for each shell. record lack of closure from centric reflection for each shell. record phasing power from acentric reflection for each shell. record phasing power from centric reflection for each shell. The mean phasing power P for reflections in this shell. sum|Fh~calc~^2^| P = (----------------------------)^1/2^ sum|Fph~obs~ - Fph~calc~|^2^ Fph~obs~ = the observed structure-factor amplitude of the derivative Fph~calc~ = the calculated structure-factor amplitude of the derivative Fh~calc~ = the calculated structure-factor amplitude from the heavy-atom model sum is taken over the specified reflections The number of reflections in this shell. The number of acentric reflections in this shell. The number of anomalous reflections in this shell. The number of centric reflections in this shell. The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. Note that the resolution limits of shells in the items attribute d_res_high in category phasing_MIR_shell and attribute d_res_low in category phasing_MIR_shell are independent of the resolution limits of shells in the items attribute d_res_high in category reflns_shell and attribute d_res_low in category reflns_shell. The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. Note that the resolution limits of shells in the items attribute d_res_high in category phasing_MIR_shell and attribute d_res_low in category phasing_MIR_shell are independent of the resolution limits of shells in the items attribute d_res_high in category reflns_shell and attribute d_res_low in category reflns_shell. Data items in the PHASING_AVERAGING category record details about the phasing of the structure where methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved. Example 1 - hypothetical example. <PDBx:phasing_averagingCategory> <PDBx:phasing_averaging entry_id="EXAMHYPO"> <PDBx:details> The position of the threefold axis was redetermined every five cycles.</PDBx:details> <PDBx:method> Iterative threefold averaging alternating with phase extensions by 0.5 reciprocal lattice units per cycle.</PDBx:method> </PDBx:phasing_averaging> </PDBx:phasing_averagingCategory> A description of special aspects of the averaging process. A description of the phase-averaging phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the phase-averaging program. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure where a model isomorphous to the structure being phased was used to generate the initial phases. Example 1 - based on PDB entry 4PHV and laboratory records for the structure corresponding to PDB entry 4PHV. <PDBx:phasing_isomorphousCategory> <PDBx:phasing_isomorphous entry_id="1ABC"> <PDBx:details> The inhibitor and all solvent atoms were removed from the parent structure before beginning refinement. All static disorder present in the parent structure was also removed.</PDBx:details> <PDBx:parent>PDB entry 5HVP</PDBx:parent> </PDBx:phasing_isomorphous> </PDBx:phasing_isomorphousCategory> A description of special aspects of the isomorphous phasing. Residues 13-18 were eliminated from the starting model as it was anticipated that binding of the inhibitor would cause a structural rearrangement in this part of the structure. A description of the isomorphous-phasing method used to phase this structure. Note that this is not the computer program used, which is described in the SOFTWARE category, but rather the method itself. This data item should be used to describe significant methodological options used within the isomorphous phasing program. Iterative threefold averaging alternating with phase extension by 0.5 reciprocal lattice units per cycle. Reference to the structure used to generate starting phases if the structure referenced in this data block was phased by virtue of being isomorphous to a known structure (e.g. a mutant that crystallizes in the same space group as the wild-type protein.) This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PHASING_SET category record details about the data sets used in a phasing experiment. A given data set may be used in a number of different ways; for instance, a single data set could be used both as an isomorphous derivative and as a component of a multiple-wavelength calculation. This category establishes identifiers for each data set and permits the archiving of a subset of experimental information for each data set (cell constants, wavelength, temperature etc.). This and related categories of data items are provided so that derivative intensity and phase information can be stored in the same data block as the information for the refined structure. If all the possible experimental information for each data set (raw data sets, crystal growth conditions etc.) is to be archived, these data items should be recorded in a separate data block. Example 1 - based on laboratory records for an Hg/Pt derivative of protein NS1. <PDBx:phasing_setCategory> <PDBx:phasing_set id="NS1-96"> <PDBx:cell_angle_alpha>90.0</PDBx:cell_angle_alpha> <PDBx:cell_angle_beta>90.0</PDBx:cell_angle_beta> <PDBx:cell_angle_gamma>90.0</PDBx:cell_angle_gamma> <PDBx:cell_length_a>38.63</PDBx:cell_length_a> <PDBx:cell_length_b>38.63</PDBx:cell_length_b> <PDBx:cell_length_c>82.88</PDBx:cell_length_c> <PDBx:detector_specific>RXII</PDBx:detector_specific> <PDBx:detector_type>image plate</PDBx:detector_type> <PDBx:radiation_wavelength>1.5145</PDBx:radiation_wavelength> </PDBx:phasing_set> </PDBx:phasing_setCategory> Unit-cell angle alpha for this data set in degrees. Unit-cell angle beta for this data set in degrees. Unit-cell angle gamma for this data set in degrees. Unit-cell length a for this data set in angstroms. Unit-cell length b for this data set in angstroms. Unit-cell length c for this data set in angstroms. The particular radiation detector. In general, this will be a manufacturer, description, model number or some combination of these. Siemens model x Kodak XG MAR Research model y The general class of the radiation detector. multiwire imaging plate CCD film The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution. The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution. The value of attribute pdbx_temp_details in category phasing_set describes any special details about the data collection temperature for this phasing data set. The particular source of radiation. In general, this will be a manufacturer, description, or model number (or some combination of these) for laboratory sources and an institution name and beamline name for synchrotron sources. Rigaku RU200 Philips fine focus Mo NSLS beamline X8C The mean wavelength of the radiation used to measure this data set. The temperature in kelvins at which the data set was measured. The value of attribute id in category phasing_set must uniquely identify a record in the PHASING_SET list. Note that this item need not be a number; it can be any unique identifier. KAu(CN)2 K2HgI4 Data items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment. This list may contain information from a number of different data sets; attribute set_id in category phasing_set_refln indicates the data set to which a given record corresponds. Example 1 - based on laboratory records for the 15,15,32 reflection of an Hg/Pt derivative of protein NS1. <PDBx:phasing_set_reflnCategory> <PDBx:phasing_set_refln index_h="15" index_k="15" index_l="32" set_id="NS1-96"> <PDBx:F_meas_au>181.79</PDBx:F_meas_au> <PDBx:F_meas_sigma_au>3.72</PDBx:F_meas_sigma_au> </PDBx:phasing_set_refln> </PDBx:phasing_set_reflnCategory> The measured value of the structure factor for this reflection in this data set in electrons. The measured value of the structure factor for this reflection in this data set in arbitrary units. The standard uncertainty (estimated standard deviation) of attribute F_meas in category phasing_set_refln in electrons. The standard uncertainty (estimated standard deviation) of attribute F_meas_au in category phasing_set_refln in arbitrary units. Miller index h of this reflection in this data set. Miller index k of this reflection in this data set. Miller index l of this reflection in this data set. This data item is a pointer to attribute id in category phasing_set in the PHASING_SET category. Data items in the PUBL category are used when submitting a manuscript for publication. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:publCategory> <PDBx:publ entry_id="1ABC"> <PDBx:section_abstract> The oxazolidinone ring is a shallow envelope conformation with the tert-butyl and iso-butyl groups occupying trans-positions with respect to the ring. The angles at the N atom sum to 356.2\&#37;, indicating a very small degree of pyramidalization at this atom. This is consistent with electron delocalization between the N atom and the carbonyl centre [N-C=O = 1.374(3)\&#37;A].</PDBx:section_abstract> <PDBx:section_title> trans-3-Benzoyl-2-(tert-butyl)-4-(iso-butyl)- 1,3-oxazolidin-5-one</PDBx:section_title> </PDBx:publ> </PDBx:publCategory> Example 2 - based on C~31~H~48~N~4~O~4~, reported by Coleman, Patrick, Andersen & Rettig [Acta Cryst. (1996), C52, 1525-1527]. <PDBx:publCategory> <PDBx:publ entry_id="1ABC"> <PDBx:section_title> Hemiasterlin methyl ester</PDBx:section_title> <PDBx:section_title_footnote> IUPAC name: methyl 2,5-dimethyl-4-{2-[3-methyl- 2-methylamino-3-(N-methylbenzo[b]pyrrol- 3-yl)butanamido]-3,3-dimethyl-N-methyl- butanamido}-2-hexenoate.</PDBx:section_title_footnote> </PDBx:publ> </PDBx:publCategory> The name and address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. It is preferable to use the separate data items _publ.contact_author_name and _publ.contact_author_address. Professor George Ferguson Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 The address of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. Department of Chemistry and Biochemistry University of Guelph Ontario Canada N1G 2W1 E-mail address in a form recognizable to international networks. The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. name@host.domain.country uur5@banjo.bitnet Facsimile telephone number of the author submitting the manuscript and data block. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended. 12(34)9477330 12()349477330 The name of the author submitting the manuscript and data block. This is the person contacted by the journal editorial staff. Professor George Ferguson Telephone number of the author submitting the manuscript and data block. The recommended style starts with the international dialing prefix, followed by the area code in parentheses, followed by the local number and any extension number prefixed by 'x', with no spaces. The earlier convention of including the international dialing prefix in parentheses is no longer recommended. 12(34)9477330 12()349477330 12(34)9477330x5543 A letter submitted to the journal editor by the contact author. A description of the word-processor package and computer used to create the word-processed manuscript stored as attribute manuscript_processed in category publ. Tex file created by FrameMaker on a Sun 3/280 The full manuscript of a paper (excluding possibly the figures and the tables) output in ASCII characters from a word processor. Information about the generation of this data item must be specified in the data item attribute manuscript_creation in category publ. The full manuscript of a paper (excluding figures and possibly the tables) output as standard ASCII text. The category of paper submitted. For submission to Acta Crystallographica Section C or Acta Crystallographica Section E, ONLY the codes indicated for use with these journals should be used. The name of the co-editor whom the authors would like to handle the submitted manuscript. The name of the journal to which the manuscript is being submitted. The abstract section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The acknowledgements section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The comment section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The discussion section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The experimental section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed. in category publ The _publ.section_exptl_prep, _publ.section_exptl_solution and attribute section_exptl_refinement in category publ items are preferred for separating the chemical preparation, structure solution and refinement aspects of the description of the experiment. The experimental preparation section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. The experimental refinement section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. The experimental solution section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. The figure captions section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The introduction section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The references section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The synopsis section of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The table legends section of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. The title of a manuscript if the manuscript is submitted in parts. As an alternative see attribute manuscript_text in category publ and attribute manuscript_processed in category publ. The footnote to the title of a manuscript if the manuscript is submitted in parts. As an alternative see _publ.manuscript_text and _publ.manuscript_processed. This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication. Example 1 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:publ_authorCategory> <PDBx:publ_author name="Willis, Anthony C."> <PDBx:address> Research School of Chemistry Australian National University GPO Box 4 Canberra, A.C.T. Australia 2601</PDBx:address> </PDBx:publ_author> </PDBx:publ_authorCategory> The address of a publication author. If there is more than one author this is looped with attribute name in category publ_author. Department Institute Street City and postcode COUNTRY The e-mail address of a publication author. If there is more than one author, this will be looped with attribute name. in category publ_author The format of e-mail addresses is given in Section 3.4, Address Specification, of Internet Message Format, RFC 2822, P. Resnick (Editor), Network Standards Group, April 2001. name@host.domain.country bm@iucr.org A footnote accompanying an author's name in the list of authors of a paper. Typically indicates sabbatical address, additional affiliations or date of decease. On leave from U. Western Australia Also at Department of Biophysics Identifier in the IUCr contact database of a publication author. This identifier may be available from the World Directory of Crystallographers (http://wdc.iucr.org). 2985 The name of a publication author. If there are multiple authors this will be looped with attribute address in category publ_author. The family name(s), followed by a comma and including any dynastic components, precedes the first names or initials. Bleary, Percival R. O'Neil, F.K. Van den Bossche, G. Yang, D.-L. Simonov, Yu.A Data items in the PUBL_BODY category permit the labelling of different text sections within the body of a paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors. Example 1 - based on a paper by R. Restori & D. Schwarzenbach [Acta Cryst. (1996), A52, 369-378]. <PDBx:publ_bodyCategory> <PDBx:publ_body element="section" label="1"> <PDBx:contents> X-ray diffraction from a crystalline material provides information on the thermally and spatially averaged electron density in the crystal...</PDBx:contents> <PDBx:format>cif</PDBx:format> <PDBx:title>Introduction</PDBx:title> </PDBx:publ_body> <PDBx:publ_body element="section" label="2"> <PDBx:contents> In the rigid-atom approximation, the dynamic electron density of an atom is described by the convolution product of the static atomic density and a probability density function, $\rho_{dyn}(\bf r) = \rho_{stat}(\bf r) * P(\bf r). \eqno(1)$</PDBx:contents> <PDBx:format>tex</PDBx:format> <PDBx:title>Theory</PDBx:title> </PDBx:publ_body> </PDBx:publ_bodyCategory> Example 2 - based on a paper by R. J. Papoular, Y. Vekhter & P. Coppens [Acta Cryst. (1996), A52, 397-407]. <PDBx:publ_bodyCategory> <PDBx:publ_body element="section" label="3"> <PDBx:contents xsi:nil="true" /> <PDBx:title> The two-channel method for retrieval of the deformation electron density</PDBx:title> </PDBx:publ_body> <PDBx:publ_body element="subsection" label="3.1"> <PDBx:contents> As the wide dynamic range involved in the total electron density...</PDBx:contents> <PDBx:title>The two-channel entropy S[\D\r(r)]</PDBx:title> </PDBx:publ_body> <PDBx:publ_body element="subsection" label="3.2"> <PDBx:contents xsi:nil="true" /> <PDBx:title>Uniform vs informative prior model densities</PDBx:title> </PDBx:publ_body> <PDBx:publ_body element="subsubsection" label="3.2.1"> <PDBx:contents> Straightforward algebra leads to expressions analogous to...</PDBx:contents> <PDBx:title>Use of uniform models</PDBx:title> </PDBx:publ_body> </PDBx:publ_bodyCategory> A text section of a paper. Code indicating the appropriate typesetting conventions for accented characters and special symbols in the text section. Title of the associated section of text. The functional role of the associated text section. Code identifying the section of text. 1 1.1 2.1.3 Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list used by the journal printing software. Example 1 - hypothetical example. <PDBx:publ_manuscript_inclCategory> <PDBx:publ_manuscript_incl entry_id="EXAMHYPO"> <PDBx:extra_defn>yes</PDBx:extra_defn> <PDBx:extra_info>to emphasise special sites</PDBx:extra_info> <PDBx:extra_item>_atom_site.symmetry_multiplicity</PDBx:extra_item> </PDBx:publ_manuscript_incl> <PDBx:publ_manuscript_incl entry_id="EXAMHYPO"> <PDBx:extra_defn>yes</PDBx:extra_defn> <PDBx:extra_info>rare material, unusual source</PDBx:extra_info> <PDBx:extra_item>_chemical.compound_source</PDBx:extra_item> </PDBx:publ_manuscript_incl> <PDBx:publ_manuscript_incl entry_id="EXAMHYPO"> <PDBx:extra_defn>yes</PDBx:extra_defn> <PDBx:extra_info>limited data is a problem here</PDBx:extra_info> <PDBx:extra_item>_reflns.d_resolution_high</PDBx:extra_item> </PDBx:publ_manuscript_incl> <PDBx:publ_manuscript_incl entry_id="EXAMHYPO"> <PDBx:extra_defn>no</PDBx:extra_defn> <PDBx:extra_info>unusual value for this material</PDBx:extra_info> <PDBx:extra_item>_crystal.magnetic_permeability</PDBx:extra_item> </PDBx:publ_manuscript_incl> </PDBx:publ_manuscript_inclCategory> Flags whether the corresponding data item marked for inclusion in a journal request list is a standard CIF definition or not. A short note indicating the reason why the author wishes the corresponding data item marked for inclusion in the journal request list to be published. to emphasise very special sites rare material from unusual source the limited data is a problem here a new data quantity needed here Specifies the inclusion of specific data into a manuscript which are not normally requested by the journal. The values of this item are the extra data names (which MUST be enclosed in single quotes) that will be added to the journal request list. _atom_site.symmetry_multiplicity _chemical.compound_source _reflns.d_resolution_high _crystal.magnetic_permeability This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the REFINE category record details about the structure-refinement parameters. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:refineCategory> <PDBx:refine entry_id="5HVP" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:ls_R_factor_obs>0.176</PDBx:ls_R_factor_obs> <PDBx:ls_number_parameters>7032</PDBx:ls_number_parameters> <PDBx:ls_number_reflns_obs>12901</PDBx:ls_number_reflns_obs> <PDBx:ls_number_restraints>6609</PDBx:ls_number_restraints> <PDBx:ls_weighting_details> Sigdel model of Konnert-Hendrickson: Sigdel: Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = -150.0 at beginning of refinement Afsig = 15.5, Bfsig = -50.0 at end of refinement</PDBx:ls_weighting_details> <PDBx:ls_weighting_scheme>calc</PDBx:ls_weighting_scheme> </PDBx:refine> </PDBx:refineCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:refineCategory> <PDBx:refine entry_id="TOZ" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:details>sfls:_F_calc_weight_full_matrix</PDBx:details> <PDBx:diff_density_max>.131</PDBx:diff_density_max> <PDBx:diff_density_min>-.108</PDBx:diff_density_min> <PDBx:ls_R_factor_all>.038</PDBx:ls_R_factor_all> <PDBx:ls_R_factor_obs>.034</PDBx:ls_R_factor_obs> <PDBx:ls_abs_structure_Flack>0</PDBx:ls_abs_structure_Flack> <PDBx:ls_abs_structure_details> The absolute configuration was assigned to agree with the known chirality at C3 arising from its precursor l-leucine.</PDBx:ls_abs_structure_details> <PDBx:ls_extinction_coef>3514</PDBx:ls_extinction_coef> <PDBx:ls_extinction_expression> Larson, A. C. (1970). &quot;Crystallographic Computing&quot;, edited by F. R. Ahmed. Eq. (22) p. 292. Copenhagen: Munksgaard.</PDBx:ls_extinction_expression> <PDBx:ls_extinction_method>Zachariasen</PDBx:ls_extinction_method> <PDBx:ls_goodness_of_fit_all>1.462</PDBx:ls_goodness_of_fit_all> <PDBx:ls_goodness_of_fit_obs>1.515</PDBx:ls_goodness_of_fit_obs> <PDBx:ls_hydrogen_treatment>refxyz except H332B noref</PDBx:ls_hydrogen_treatment> <PDBx:ls_matrix_type>full</PDBx:ls_matrix_type> <PDBx:ls_number_constraints>0</PDBx:ls_number_constraints> <PDBx:ls_number_parameters>272</PDBx:ls_number_parameters> <PDBx:ls_number_reflns_obs>1408</PDBx:ls_number_reflns_obs> <PDBx:ls_number_restraints>0</PDBx:ls_number_restraints> <PDBx:ls_shift_over_esd_max>.535</PDBx:ls_shift_over_esd_max> <PDBx:ls_shift_over_esd_mean>.044</PDBx:ls_shift_over_esd_mean> <PDBx:ls_structure_factor_coef>F</PDBx:ls_structure_factor_coef> <PDBx:ls_wR_factor_all>.044</PDBx:ls_wR_factor_all> <PDBx:ls_wR_factor_obs>.042</PDBx:ls_wR_factor_obs> <PDBx:ls_weighting_details>w=1/(\s^2^(F)+0.0004F^2^)</PDBx:ls_weighting_details> <PDBx:ls_weighting_scheme>calc</PDBx:ls_weighting_scheme> </PDBx:refine> </PDBx:refineCategory> The maximum isotropic displacement parameter (B value) found in the coordinate set. The mean isotropic displacement parameter (B value) for the coordinate set. The minimum isotropic displacement parameter (B value) found in the coordinate set. The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. The [1][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure. The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections included in the refinement The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections). The correlation coefficient is scale-independent and gives an idea of the quality of the refined model. sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>) R~corr~ = ------------------------------------------------------------ SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^} Fo = observed structure factors Fc = calculated structure factors <> denotes average value summation is over reflections not included in the refinement (free reflections) Description of special aspects of the refinement process. The maximum value of the electron density in the final difference Fourier map. The standard uncertainty (estimated standard deviation) of attribute diff_density_max in category refine. The minimum value of the electron density in the final difference Fourier map. The standard uncertainty (estimated standard deviation) of attribute diff_density_min in category refine. The root-mean-square-deviation of the electron density in the final difference Fourier map. This value is measured with respect to the arithmetic mean density and is derived from summations over each grid point in the asymmetric unit of the cell. This quantity is useful for assessing the significance of the values of _refine.diff_density_min and _refine.diff_density_max, and also for defining suitable contour levels. The standard uncertainty (estimated standard deviation) of attribute diff_density_rms in category refine. Residual factor R(Fsqd) for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, calculated on the squares of the observed and calculated structure-factor amplitudes. sum|F~obs~^2^ - F~calc~^2^| R(Fsqd) = --------------------------- sum|F~obs~^2^| F~obs~^2^ = squares of the observed structure-factor amplitudes F~calc~^2^ = squares of the calculated structure-factor amplitudes sum is taken over the specified reflections Residual factor R(I) for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, calculated on the estimated reflection intensities. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum|I~obs~ - I~calc~| R(I) = --------------------- sum|I~obs~| I~obs~ = the net observed intensities I~calc~ = the net calculated intensities sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections The estimated error in attribute ls_R_factor_R_free. in category refine The method used to estimate the error is described in the item attribute ls_R_factor_R_free_error_details in category refine. Special aspects of the method used to estimated the error in attribute ls_R_factor_R_free in category refine. Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns attribute ls_R_factor_obs in category refine should not be confused with attribute ls_R_factor_R_work in category refine; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in attribute details. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections Residual factor R for all reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections Residual factor for the reflections (with number given by attribute number_gt) in category reflns judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. The reflections also satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine. This is the conventional R factor. See also attribute ls_wR_factor_ in category refine definitions. sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion. in category reflns attribute ls_R_factor_obs in category refine should not be confused with attribute ls_R_factor_R_work in category refine; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in attribute details. in category refine sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections The measure of absolute structure (enantiomorph or polarity) as defined by Flack (1983). For centrosymmetric structures, the only permitted value, if the data name is present, is 'inapplicable', represented by '.' . For noncentrosymmetric structures the value must lie in the 99.97% Gaussian confidence interval -3u =< x =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [0.0:1.0] is correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u). Ref: Flack, H. D. (1983). Acta Cryst. A39, 876-881. The standard uncertainty (estimated standard deviation) of attribute ls_abs_structure_Flack in category refine. The measure of absolute structure (enantiomorph or polarity) as defined by Rogers. The value must lie in the 99.97% Gaussian confidence interval -1 -3u =< \h =< 1 + 3u and a standard uncertainty (estimated standard deviation) u must be supplied. The item range of [-1.0, 1.0] is correctly interpreted as meaning (-1.0 - 3u) =< \h =< (1.0 + 3u). Ref: Rogers, D. (1981). Acta Cryst. A37, 734-741. The standard uncertainty (estimated standard deviation) of attribute ls_abs_structure_Rogers in category refine. The nature of the absolute structure and how it was determined. For example, this may describe the Friedel pairs used. The smallest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the highest resolution. The largest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the lowest resolution. The extinction coefficient used to calculate the correction factor applied to the structure-factor data. The nature of the extinction coefficient is given in the definitions of attribute ls_extinction_expression in category refine and attribute ls_extinction_method. in category refine For the 'Zachariasen' method it is the r* value; for the 'Becker-Coppens type 1 isotropic' method it is the 'g' value, and for 'Becker-Coppens type 2 isotropic' corrections it is the 'rho' value. Note that the magnitude of these values is usually of the order of 10000. Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-47, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558-564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. Zachariasen coefficient r* = 0.347 E04 3472 The standard uncertainty (estimated standard deviation) of attribute ls_extinction_coef in category refine. A description of or reference to the extinction-correction equation used to apply the data item attribute ls_extinction_coef in category refine. This information must be sufficient to reproduce the extinction-correction factors applied to the structure factors. Larson, A. C. (1970). "Crystallographic Computing", edited by F. R. Ahmed. Eq. (22), p.292. Copenhagen: Munksgaard. A description of the extinction-correction method applied. This description should include information about the correction method, either 'Becker-Coppens' or 'Zachariasen'. The latter is sometimes referred to as the 'Larson' method even though it employs Zachariasen's formula. The Becker-Coppens procedure is referred to as 'type 1' when correcting secondary extinction dominated by the mosaic spread; as 'type 2' when secondary extinction is dominated by particle size and includes a primary extinction component; and as 'mixed' when there is a mixture of types 1 and 2. For the Becker-Coppens method, it is also necessary to set the mosaic distribution as either 'Gaussian' or 'Lorentzian' and the nature of the extinction as 'isotropic' or 'anisotropic'. Note that if either the 'mixed' or 'anisotropic' corrections are applied, the multiple coefficients cannot be contained in *_extinction_coef and must be listed in attribute details. in category refine Ref: Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129-147, 148-153. Zachariasen, W. H. (1967). Acta Cryst. 23, 558- 564. Larson, A. C. (1967). Acta Cryst. 23, 664-665. B-C type 2 Gaussian isotropic The least-squares goodness-of-fit parameter S for all data after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of attribute ls_restrained_S_all. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections The standard uncertainty (estimated standard deviation) of attribute ls_goodness_of_fit_all in category refine. The least-squares goodness-of-fit parameter S for significantly intense reflections (see attribute threshold_expression) in category reflns after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also attribute ls_restrained_S_ in category refine definitions. { sum { w [ Y(obs) - Y(calc) ]^2^ } }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections The least-squares goodness-of-fit parameter S for reflection data classified as 'observed' (see attribute observed_criterion) in category reflns after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also the definition of attribute ls_restrained_S_obs. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ S = ( ---------------------------- ) ( N~ref~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] N~ref~ = the number of reflections used in the refinement N~param~ = the number of refined parameters sum is taken over the specified reflections The standard uncertainty (estimated standard deviation) of attribute ls_goodness_of_fit_obs in category refine. The least-squares goodness-of-fit parameter S for all reflections included in the refinement after the final cycle of refinement. Ideally, account should be taken of parameters restrained in the least-squares refinement. See also _refine_ls_restrained_S_ definitions. { sum | w | Y(obs) - Y(calc) |^2^ | }^1/2^ S = { ----------------------------------- } { Nref - Nparam } Y(obs) = the observed coefficients (see _refine_ls_structure_factor_coef) Y(calc) = the calculated coefficients (see _refine_ls_structure_factor_coef) w = the least-squares reflection weight [1/(u^2^)] u = standard uncertainty Nref = the number of reflections used in the refinement Nparam = the number of refined parameters and the sum is taken over the specified reflections Treatment of hydrogen atoms in the least-squares refinement. Type of matrix used to accumulate the least-squares derivatives. The number of constrained (non-refined or dependent) parameters in the least-squares process. These may be due to symmetry or any other constraint process (e.g. rigid-body refinement). See also _atom_site.constraints and _atom_site.refinement_flags. A general description of constraints may appear in attribute details in category refine. The number of parameters refined in the least-squares process. If possible, this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns. The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Restrained parameters often involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site.refinement_flags. A general description of refinement constraints may appear in attribute details in category refine. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy the same limits. The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by attribute observed_criterion in category reflns to the number of crystallographically unique reflections that satisfy the same limits. The least-squares goodness-of-fit parameter S' for all reflections after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of attribute ls_goodness_of_fit_all. in category refine ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see attribute ls_number_reflns_obs) in category refine N~restr~ = the number of restraints (see attribute ls_number_restraints) in category refine N~param~ = the number of refined parameters (see attribute ls_number_parameters) in category refine sum is taken over the specified reflections sumr is taken over the restraints The least-squares goodness-of-fit parameter S' for reflection data classified as observed (see attribute observed_criterion) in category reflns after the final cycle of least-squares refinement. This parameter explicitly includes the restraints applied in the least-squares process. See also the definition of attribute ls_goodness_of_fit_obs. in category refine ( sum |w |Y~obs~ - Y~calc~|^2^| )^1/2^ ( + sum~r~|w~r~ |P~calc~ - P~targ~|^2^| ) S' = ( ------------------------------------- ) ( N~ref~ + N~restr~ - N~param~ ) Y~obs~ = the observed coefficients (see attribute ls_structure_factor_coef) in category refine Y~calc~ = the calculated coefficients (see attribute ls_structure_factor_coef) in category refine w = the least-squares reflection weight [1/(e.s.d. squared)] P~calc~ = the calculated restraint values P~targ~ = the target restraint values w~r~ = the restraint weight N~ref~ = the number of reflections used in the refinement (see attribute ls_number_reflns_obs) in category refine N~restr~ = the number of restraints (see attribute ls_number_restraints) in category refine N~param~ = the number of refined parameters (see attribute ls_number_parameters) in category refine sum is taken over the specified reflections sumr is taken over the restraints The largest ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation). The average ratio of the final least-squares parameter shift to the final standard uncertainty (estimated standard deviation). The largest ratio of the final least-squares parameter shift to the final standard uncertainty. An upper limit for the largest ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the largest value of the shift divided by the final standard uncertainty is too small to measure. The average ratio of the final least-squares parameter shift to the final standard uncertainty. An upper limit for the average ratio of the final least-squares parameter shift to the final standard uncertainty. This item is used when the average value of the shift divided by the final standard uncertainty is too small to measure. Structure-factor coefficient |F|, F^2^ or I used in the least- squares refinement process. Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections Weighted residual factor wR for all reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low. in category refine ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections A description of special aspects of the weighting scheme used in least-squares refinement. Used to describe the weighting when the value of attribute ls_weighting_scheme in category refine is specified as 'calc'. Sigdel model of Konnert-Hendrickson: Sigdel = Afsig + Bfsig*(sin(theta)/lambda-1/6) Afsig = 22.0, Bfsig = 150.0 at the beginning of refinement. Afsig = 16.0, Bfsig = 60.0 at the end of refinement. The weighting scheme applied in the least-squares process. The standard code may be followed by a description of the weight (but see attribute ls_weighting_details in category refine for a preferred approach). The maximum value for occupancy found in the coordinate set. The minimum value for occupancy found in the coordinate set. Average figure of merit of phases of reflections not included in the refinement. This value is derived from the likelihood function. FOM = I~1~(X)/I~0~(X) I~0~, I~1~ = zero- and first-order modified Bessel functions of the first kind X = sigma~A~ |E~o~| |E~c~|/SIGMA E~o~, E~c~ = normalized observed and calculated structure factors sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = form factor of atoms delta~x~ = expected error SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. Average figure of merit of phases of reflections included in the refinement. This value is derived from the likelihood function. FOM = I~1~(X)/I~0~(X) I~0~, I~1~ = zero- and first-order modified Bessel functions of the first kind X = sigma~A~ |E~o~| |E~c~|/SIGMA E~o~, E~c~ = normalized observed and calculated structure factors sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = form factor of atoms delta~x~ = expected error SIGMA = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = uncertainties of normalized observed structure factors epsilon = multiplicity of the diffracting plane Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on a maximum-likelihood residual. The overall standard uncertainty (sigma~B~)^2^ gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 8 ---------------------------------------------- sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^4^} N~a~ = number of atoms E~o~ = normalized structure factors m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector SUM_AS = (sigma~A~)^2^/Sigma^2^ Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = experimental uncertainties of normalized structure factors sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = atom form factor delta~x~ = expected error epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma~A~ estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU B estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html The overall standard uncertainty (estimated standard deviation) of the positional parameters based on a maximum likelihood residual. The overall standard uncertainty (sigma~X~)^2^ gives an idea of the uncertainty in the position of averagely defined atoms (atoms with B values equal to average B value) 3 N~a~ (sigma~X~)^2^ = --------------------------------------------------------- 8 pi^2^ sum~i~ {[1/Sigma - (E~o~)^2^ (1-m^2^)](SUM_AS)s^2^} N~a~ = number of atoms E~o~ = normalized structure factors m = figure of merit of phases of reflections included in the summation s = reciprocal-space vector SUM_AS = (sigma~A~)^2^/Sigma^2^ Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^] sigma~{E;exp}~ = experimental uncertainties of normalized structure factors sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~) estimated using maximum likelihood Sigma~P~ = sum~{atoms in model}~ f^2^ Sigma~N~ = sum~{atoms in crystal}~ f^2^ f = atom form factor delta~x~ = expected error epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Ref: (sigma_A estimation) "Refinement of macromolecular structures by the maximum-likelihood method", Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255. (SU ML estimation) Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 0.65 ---------- (R~value~)^2^ (D~min~)^2^ C^-2/3^ (N~o~-N~p~) N~a~ = number of atoms included in refinement N~o~ = number of observations N~p~ = number of parameters refined R~value~ = conventional crystallographic R value D~min~ = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the free R value. The overall standard uncertainty (sigma~B~) gives an idea of the uncertainty in the B values of averagely defined atoms (atoms with B values equal to the average B value). N~a~ (sigma~B~)^2^ = 0.65 ---------- (R~free~)^2^ (D~min~)^2^ C^-2/3^ (N~o~-N~p~) N~a~ = number of atoms included in refinement N~o~ = number of observations N~p~ = number of parameters refined R~free~ = conventional free crystallographic R value calculated using reflections not included in refinement D~min~ = maximum resolution C = completeness of data Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. Murshudov, G. N. & Dodson, E. J. (1997). Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newsletter on Protein Crystallography, No. 33, January 1997, pp. 31-39. http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html Details of the manner in which the cross validation reflections were selected. Random selection The crystallographic reliability index Rcomplete for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion in category reflns Ref: Luebben, J., Gruene, T., (2015). Proc.Nat.Acad.Sci. 112(29) 8999-9003 A flag for TLS refinements identifying the type of atomic displacement parameters stored in attribute B_iso_or_equiv in category atom_site. Average Fourier Shell Correlation (avgFSC) between model and observed structure factors for reflections not included in refinement. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~free-i~) avgFSC~free~ = --------------------- sum(N~i~) N~i~ = the number of free reflections in the resolution shell i FSC~free-i~ = FSC for free reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~free-i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~free-i~ is carried over all free reflections in the resolution shell. Summation of avgFSC~free~ is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). Overall average Fourier Shell Correlation (avgFSC) between model and observed structure factors for all reflections. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~i~) avgFSC = ---------------- sum(N~i~) N~i~ = the number of all reflections in the resolution shell i FSC~i~ = FSC for all reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~i~ is carried over all reflections in the resolution shell. Summation of avgFSC is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). Average Fourier Shell Correlation (avgFSC) between model and observed structure factors for reflections included in refinement. The average FSC is a measure of the agreement between observed and calculated structure factors. sum(N~i~ FSC~work-i~) avgFSC~work~ = --------------------- sum(N~i~) N~i~ = the number of working reflections in the resolution shell i FSC~work-i~ = FSC for working reflections in the i-th resolution shell calculated as: (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~work-i~ = ------------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation of FSC~work-i~ is carried over all working reflections in the resolution shell. Summation of avgFSC~work~ is carried over all resolution shells. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). Value of F at "high end" of data cutoff. 17600 Value of RMS |F| used as high data cutoff. 205.1 Value of F at "low end" of data cutoff. 0.30 The density correlation coefficient is calculated from atomic densities of (2Fobs-Fcalc) map - "Robs" and the model map (Fcalc) - "Rcalc" : D_corr = <Robs><Rcalc>/sqrt(<Robs**2><Rcalc**2>) where <Robs> is the mean of "observed" densities of all atoms <Rcalc> is the mean of "calculated" densities of all atoms. The value of density for some atom from map R(x) is: sum_i ( R(xi) * Ratom(xi - xa) ) Dens = ---------------------------------- sum_i ( Ratom(xi - xa) ) where Ratom(x) is atomic electron density for the x-th grid point. xa - vector of the centre of atom. xi - vector of the i-th point of grid. Sum is taken over all grid points which have distance from the center of the atom less than the Radius_limit. For all atoms Radius_limit = 2.5 A. Ref: Vaguine, A.A., Richelle, J. & Wodak, S.J. (1999). Acta Cryst. D55,199-205 An identifier for the diffraction data set used in this refinement. Multiple diffraction data sets specified as a comma separated list. Whether the structure was refined with indvidual isotropic, anisotropic or overall temperature factor. Isotropic Overall Whether the cross validataion method was used through out or only at the end. FREE R-VALUE Data cutoff (SIGMA(F)) Data cutoff (SIGMA(F^2)) Data cutoff (SIGMA(I)) Method(s) used to determine the structure. AB INITIO PHASING Direct Methods DM Iterative Single wavelength Anomalous Scattering ISAS Iterative Single Isomorphous Replacement ISIR Iterative Single Isomorphous Replacement with Anomalous Scattering ISIRAS Multi wavelength Anomalous Diffraction MAD Multiple Isomorphous Replacement MIR Multiple Isomorphous Replacement with Anomalous Scattering MIRAS Molecular Replacement MR Single Isomorphous Replacement SIR Single Isomorphous Replacement with Anomalous Scattering SIRAS Overall estimated standard uncertainties of thermal parameters based on Maximum likelihood residual. Overall ESU gives an idea about uncertainties of B-values of averagely defined atoms (atoms with B-values equal to average B-value) N_a (sigma_B)^2 = 8 ---------------------------------------------- sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^4} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is form factor of atoms delta_x = expected error m = is figure of merit of phases of reflection included in summation delta_x expected error s = reciprocal space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Reference for sigma_A estimation: "Refinement of Macromolecular Structures by the Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255 Reference for ESU_ML estimation: "Simplified error estimation a la Cruickshank in macromolecular crystallography", Murshudov G.N. & Dodson E.J. in the "CCP4 Newsletter on protein crystallography" Number 33 ed. M.Winn Overall estimated standard uncertainties of positional parameters based on Maximum likelihood residual. Overall ESU gives an idea about uncertainties in the position of averagely defined atoms (atoms with B-values equal to average B-value) 3 N_a (sigma_X)^2 = ----------------------------------------------------- 8 pi^2 sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^2} SUM_AS = (sigma_A)^2/Sigma^2) N_a = number of atoms Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2) E_o = normalized structure factors sigma_{E;exp} = experimental uncertainties of normalized structure factors sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N) estimated using maximum likelihood Sigma_P = sum_{atoms in model} f^2 Sigma_N = sum_{atoms in crystal} f^2 f = is formfactor of atoms delta_x = expected error m = is figure of merit of phases of reflection included in summation delta_x expected error s = reciprocal space vector epsilon = multiplicity of diffracting plane summation is over all reflections included in refinement Reference for sigma_A estimation: "Refinement of Macromolecular Structures by the Maximum-Likelihood Method:" G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997) Acta Crystallogr. D53, 240-255 Reference for ESU_ML estimation: Simplified error estimation a la Cruickshank in macromolecular crystallograpy Murshudov G.N. & Dodson E.J. in the "CCP4 Newsletter on protein crystallography" Number 33 ed. M.Winn Overall estimated standard uncertainties of positional parameters based on R value. Overall estimated standard uncertainties of positional parameters based on R free value. The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Blow, D (2002) Acta Cryst. D58, 792-797 The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R-free value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Blow, D (2002) Acta Cryst. D58, 792-797 The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R-free value, expressed in a formalism known as the dispersion precision indicator (DPI). Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601. The overall phase error for all reflections after refinement using the current refinement target. 0.30 Residual factor R for reflections that satisfy the resolution limits established by attribute ls_d_res_high in category refine and attribute ls_d_res_low in category refine and the observation limit established by attribute observed_criterion. in category reflns sum|F~obs~**2 - F~calc~**2| R = --------------------- sum|F~obs~**2| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement. This correlation factor is found in the fitting using the Levenberg-Marquardt algorithm to search for the minimum value of chisquare. Almost all computer codes for Rietveld refinement employ the Gauss-Newton algorithm to find parameters which minimize the weighted sum of squares of the residuals. A description of the equations is given on http://www.water.hut.fi/~tkarvone/fr_org_s.htm The least squares refinement "band matrix" approximation to the full matrix. The total number of points in the measured diffractogram. The total number of data points in the processed diffractogram. The total number of powder patterns used. Rietveld/Profile fit R factors. Note that the R factor computed for Rietveld refinements using the extracted reflection intensity values (often called the Rietveld or Bragg R factor, R~B~) is not properly a profile R factor. pdbx_pd_proc_ls_prof_R_factor, often called R~p~, is an unweighted fitness metric for the agreement between the observed and computed diffraction patterns R~p~ = sum~i~ | I~obs~(i) - I~calc~(i) | / sum~i~ ( I~obs~(i) ) Note that in the above equations, w(i) is the weight for the ith data point I~obs~(i) is the observed intensity for the ith data point, sometimes referred to as y~i~(obs) or y~oi~. I~calc~(i) is the computed intensity for the ith data point with background and other corrections applied to match the scale of the observed dataset, sometimes referred to as y~i~(calc) or y~ci~. n is the total number of data points (see attribute pdbx_pd_number_of_points) in category refine less the number of data points excluded from the refinement. p is the total number of refined parameters. Rietveld/Profile fit R factors. Note that the R factor computed for Rietveld refinements using the extracted reflection intensity values (often called the Rietveld or Bragg R factor, R~B~) is not properly a profile R factor. pdbx_pd_proc_ls_prof_wR_factor often called R~wp~, is a weighted fitness metric for the agreement between the observed and computed diffraction patterns R~wp~ = SQRT { sum~i~ ( w(i) [ I~obs~(i) - I~calc~(i) ]^2^ ) / sum~i~ ( w(i) [I~obs~(i)]^2^ ) } Note that in the above equations, w(i) is the weight for the ith data point I~obs~(i) is the observed intensity for the ith data point, sometimes referred to as y~i~(obs) or y~oi~. I~calc~(i) is the computed intensity for the ith data point with background and other corrections applied to match the scale of the observed dataset, sometimes referred to as y~i~(calc) or y~ci~. n is the total number of data points (see attribute pdbx_pd_number_of_points) in category refine less the number of data points excluded from the refinement. p is the total number of refined parameters. Real space R factor of electron density for all atoms. The real space R factor is calculated by the equation R_real = [Sum~i (|Dobs - Dcal|)]/[Sum~i (|Dobs + Dcal|)] Where: Dobs is the observed electron density, Dcal is the calculated electron density, summation is for all the grid points Ref: Branden, C.I. & Jones, T.A. (1990). Nature, 343, 687-689 For bulk solvent mask calculation, the amount that the ionic radii of atoms, which can be ions, are increased used. For bulk solvent mask calculation, amount mask is shrunk after taking away atoms with new radii and a constant value assigned to this new region. For bulk solvent mask calculation, the value by which the vdw radii of non-ion atoms (like carbon) are increased and used. Starting model for refinement. Starting model for molecular replacement should refer to a previous structure or experiment. BDL001 Special case of stereochemistry target values used in SHELXL refinement. Stereochemistry target values used in refinement. Special aspects of the solvent model used during refinement. The value of the BSOL solvent-model parameter describing the average isotropic displacement parameter of disordered solvent atoms. This is one of the two parameters (the other is attribute solvent_model_param_ksol) in category refine in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. The value of the KSOL solvent-model parameter describing the ratio of the electron density in the bulk solvent to the electron density in the molecular solute. This is one of the two parameters (the other is attribute solvent_model_param_bsol) in category refine in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)] where k0 and B0 are the scale factors for the protein. Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268. This data item is a pointer to attribute id in category entry in the ENTRY category. This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine can be used to distinguish the results of joint refinements. Data items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:refine_B_isoCategory> <PDBx:refine_B_iso class="protein" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:treatment>isotropic</PDBx:treatment> </PDBx:refine_B_iso> <PDBx:refine_B_iso class="solvent" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:treatment>isotropic</PDBx:treatment> </PDBx:refine_B_iso> <PDBx:refine_B_iso class="inhibitor" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:treatment>isotropic</PDBx:treatment> </PDBx:refine_B_iso> </PDBx:refine_B_isoCategory> A description of special aspects of the isotropic B-factor (displacement-parameter) refinement for the class of atoms described in attribute class in category refine_B_iso. The temperature factors of atoms in the side chain of Arg 92 were held fixed due to unstable behavior in refinement. Residue name of those residues treated similarly for isotropic B (temperature) factor refinement. G A Resiude number of residues treated similarly for isotropic B (temperature) factor refinement. A B Asym chain id of residues treated similarly for isotropic B (temperature) factor refinement. A B The treatment of isotropic B-factor (displacement-parameter) refinement for a class of atoms defined in attribute class in category refine_B_iso. The value of the isotropic B factor (displacement parameter) assigned to a class of atoms defined in attribute class. in category refine_B_iso Meaningful only for atoms with fixed isotropic B factors. A class of atoms treated similarly for isotropic B-factor (displacement-parameter) refinement. all protein solvent sugar-phosphate backbone This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_B_iso can be used to distinguish the results of joint refinements. Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality. A given computer program may or may not produce values corresponding to these data names. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:refine_analyzeCategory> <PDBx:refine_analyze entry_id="5HVP" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:Luzzati_coordinate_error_obs>0.056</PDBx:Luzzati_coordinate_error_obs> <PDBx:Luzzati_d_res_low_obs>2.51</PDBx:Luzzati_d_res_low_obs> </PDBx:refine_analyze> </PDBx:refine_analyzeCategory> The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. The estimated coordinate error obtained from the plot of the R value versus sin(theta)/lambda for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. The value of the low-resolution cutoff used in constructing the Luzzati plot for reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. The value of sigma~a~ used in constructing the Luzzati plot for the reflections treated as a test set during refinement. Details of the estimation of sigma~a~ can be specified in attribute Luzzati_sigma_a_free_details. in category refine_analyze Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. Details of the estimation of sigma~a~ for the reflections treated as a test set during refinement. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. The value of sigma~a~ used in constructing the Luzzati plot for reflections classified as observed. Details of the estimation of sigma~a~ can be specified in attribute Luzzati_sigma_a_obs_details. in category refine_analyze Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. Special aspects of the estimation of sigma~a~ for the reflections classified as observed. Ref: Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810. The value of the high-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in attribute RG_work in category refine_analyze and attribute RG_free. in category refine_analyze Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. The value of the low-resolution cutoff in angstroms used in the calculation of the Hamilton generalized R factor (RG) stored in attribute RG_work in category refine_analyze and attribute RG_free. in category refine_analyze Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by attribute RG_d_res_high in category refine_analyze and attribute RG_d_res_low in category refine_analyze for the free R set of reflections that were excluded from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. The observed ratio of RGfree to RGwork. The expected RG ratio is the value that should be achievable at the end of a structure refinement when only random uncorrelated errors exist in the data and the model provided that the observations are properly weighted. When compared with the observed RG ratio it may indicate that a structure has not reached convergence or a model has been over-refined with no corresponding improvement in the model. In an unrestrained refinement, the ratio of RGfree to RGwork with only random uncorrelated errors at convergence depends only on the number of reflections and the number of parameters according to sqrt[(f + m) / (f - m) ] where f = the number of included structure amplitudes and target distances, and m = the number of parameters being refined. In the restrained case, RGfree is calculated from a random selection of residuals including both structure amplitudes and restraints. When restraints are included in the refinement, the RG ratio requires a term for the contribution to the minimized residual at convergence, D~restr~, due to those restraints: D~restr~ = r - sum [w_i . (a_i)^t . (H)^-1 a_i] where r is the number of geometrical, displacement-parameter and other restraints H is the (m,m) normal matrix given by A^t.W.A W is the (n,n) symmetric weight matrix of the included observations A is the least-squares design matrix of derivatives of order (n,m) a_i is the ith row of A Then the expected RGratio becomes sqrt [ (f + (m - r + D~restr~))/ (f - (m - r + D~restr~)) ] There is no data name for the expected value of RGfree/RGwork yet. Ref: Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Acta Cryst. D54, 547-557. The Hamilton generalized R factor for all reflections that satisfy the resolution limits established by attribute RG_d_res_high in category refine_analyze and attribute RG_d_res_low in category refine_analyze and for those reflections included in the working set when a free R set of reflections is omitted from the refinement. sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j) RG = Sqrt( ----------------------------------------------------------------- ) sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j where |Fobs| = the observed structure-factor amplitudes |Fcalc| = the calculated structure-factor amplitudes G = the scale factor which puts |Fcalc| on the same scale as |Fobs| w_{i,j} = the weight for the combination of the reflections i and j. sum_i and sum_j are taken over the specified reflections When the covariance of the amplitudes of reflection i and reflection j is zero (i.e. the reflections are independent) w{i,i} can be redefined as w_i and the nested sums collapsed into one sum. sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 RG = Sqrt( ----------------------------------- ) sum_i w_i |Fobs|_i^2 Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510. The number of discretely disordered residues in the refined model. The sum of the occupancies of the hydrogen atoms in the refined model. The sum of the occupancies of the non-hydrogen atoms in the refined model. record the high resolution for calculating Luzzati statistics. This data item is a pointer to attribute id in category entry in the ENTRY category. This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_analyze can be used to distinguish the results of joint refinements. Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement. Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. <PDBx:refine_funct_minimizedCategory> <PDBx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Amplitude)^2"> <PDBx:number_terms>3009</PDBx:number_terms> <PDBx:residual>1621.3</PDBx:residual> </PDBx:refine_funct_minimized> <PDBx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Plane+Rigid)^2"> <PDBx:number_terms>85</PDBx:number_terms> <PDBx:residual>56.68</PDBx:residual> </PDBx:refine_funct_minimized> <PDBx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(Distance)^2"> <PDBx:number_terms>1219</PDBx:number_terms> <PDBx:residual>163.59</PDBx:residual> </PDBx:refine_funct_minimized> <PDBx:refine_funct_minimized pdbx_refine_id="X-RAY DIFFRACTION" type="sum(W*Delta(U-tempfactors)^2"> <PDBx:number_terms>1192</PDBx:number_terms> <PDBx:residual>69.338</PDBx:residual> </PDBx:refine_funct_minimized> </PDBx:refine_funct_minimizedCategory> The number of observations in this term. For example, if the term is a residual of the X-ray intensities, this item would contain the number of reflections used in the refinement. The residual for this term of the function that was minimized during the refinement. The weight applied to this term of the function that was minimized during the refinement. This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_funct_minimized can be used to distinguish the results of joint refinements. The type of the function being minimized. Data items in the REFINE_HIST category record details about the steps during the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics. Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. <PDBx:refine_histCategory> <PDBx:refine_hist cycle_id="C134" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:R_factor_R_free>.274</PDBx:R_factor_R_free> <PDBx:R_factor_R_work>.160</PDBx:R_factor_R_work> <PDBx:R_factor_all>.265</PDBx:R_factor_all> <PDBx:R_factor_obs>.195</PDBx:R_factor_obs> <PDBx:d_res_high>1.85</PDBx:d_res_high> <PDBx:d_res_low>20.0</PDBx:d_res_low> <PDBx:details> Add majority of solvent molecules. B factors refined by group. Continued to remove misplaced water molecules.</PDBx:details> <PDBx:number_atoms_solvent>217</PDBx:number_atoms_solvent> <PDBx:number_atoms_total>808</PDBx:number_atoms_total> <PDBx:number_reflns_R_free>476</PDBx:number_reflns_R_free> <PDBx:number_reflns_R_work>4410</PDBx:number_reflns_R_work> <PDBx:number_reflns_all>6174</PDBx:number_reflns_all> <PDBx:number_reflns_obs>4886</PDBx:number_reflns_obs> </PDBx:refine_hist> </PDBx:refine_histCategory> Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low. in category refine_hist sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation criterion established by attribute observed_criterion. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections The lowest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the highest resolution. The highest value for the interplanar spacings for the reflection data for this cycle of refinement. This is called the lowest resolution. A description of special aspects of this cycle of the refinement process. Residues 13-17 fit and added to model; substantial rebuilding of loop containing residues 43-48; addition of first atoms to solvent model; ten cycles of Prolsq refinement. The number of solvent atoms that were included in the model at this cycle of the refinement. The total number of atoms that were included in the model at this cycle of the refinement. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_hist and attribute d_res_low in category refine_hist and the observation criterion established by attribute observed_criterion in category reflns. Mean isotropic B-value for ligand molecules included in refinement. Mean isotropic B-value for solvent molecules included in refinement. Number of carbohydrate atoms included in refinement Number of ligand atoms included in refinement Number of lipid atoms included in refinement Number of nucleic atoms included in refinement Number of protein atoms included in refinement Number of solvent atoms used in refinement Number of atoms used in refinement Total number of polymer residues included in refinement. Details of pseduo atoms used to model unexplained density The value of attribute cycle_id in category refine_hist must uniquely identify a record in the REFINE_HIST list. Note that this item need not be a number; it can be any unique identifier. This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_hist can be used to distinguish the results of joint refinements. Data items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately. Example 1 - data for a modulated structure from van Smaalen [J. Phys. Condens. Matter (1991), 3, 1247-1263]. <PDBx:refine_ls_classCategory> <PDBx:refine_ls_class code="Main"> <PDBx:R_factor_gt>0.057</PDBx:R_factor_gt> </PDBx:refine_ls_class> <PDBx:refine_ls_class code="Com"> <PDBx:R_factor_gt>0.074</PDBx:R_factor_gt> </PDBx:refine_ls_class> <PDBx:refine_ls_class code="NbRefls"> <PDBx:R_factor_gt>0.064</PDBx:R_factor_gt> </PDBx:refine_ls_class> <PDBx:refine_ls_class code="LaRefls"> <PDBx:R_factor_gt>0.046</PDBx:R_factor_gt> </PDBx:refine_ls_class> <PDBx:refine_ls_class code="Sat1"> <PDBx:R_factor_gt>0.112</PDBx:R_factor_gt> </PDBx:refine_ls_class> <PDBx:refine_ls_class code="Sat2"> <PDBx:R_factor_gt>0.177</PDBx:R_factor_gt> </PDBx:refine_ls_class> </PDBx:refine_ls_classCategory> For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors, for the reflections judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~ sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. For each reflection class, the residual factor for all reflections satisfying the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of attribute wR_factor_all. in category refine_ls_class sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. For each reflection class, the residual factor for significantly intense reflections (see attribute threshold_expression) in category reflns included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. This is the conventional R factor. See also the definition of attribute wR_factor_all. in category refine_ls_class sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. For each reflection class, the lowest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution. For each reflection class, the highest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution. For each reflection class, the weighted residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _refine_ls_class.d_res_high and _refine_ls_class.d_res_low. See also the attribute R_factor_ in category refine_ls_class definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y(calc) = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight and the sum is taken over the reflections of this class. The code identifying a certain reflection class. This code must match a attribute code in category reflns_class. 1 m1 s2 Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:refine_ls_restrCategory> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="bond_d"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>0.018</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.020</PDBx:dev_ideal_target> <PDBx:number>1654</PDBx:number> <PDBx:rejects>22</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="angle_d"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>0.038</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.030</PDBx:dev_ideal_target> <PDBx:number>2246</PDBx:number> <PDBx:rejects>139</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar_d"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>0.043</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.040</PDBx:dev_ideal_target> <PDBx:number>498</PDBx:number> <PDBx:rejects>21</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>0.015</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.020</PDBx:dev_ideal_target> <PDBx:number>270</PDBx:number> <PDBx:rejects>1</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="chiral"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>0.177</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.150</PDBx:dev_ideal_target> <PDBx:number>278</PDBx:number> <PDBx:rejects>2</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="singtor_nbd"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>0.216</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target> <PDBx:number>582</PDBx:number> <PDBx:rejects>0</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="multtor_nbd"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>0.207</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target> <PDBx:number>419</PDBx:number> <PDBx:rejects>0</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="xyhbond_nbd"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>0.245</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.500</PDBx:dev_ideal_target> <PDBx:number>149</PDBx:number> <PDBx:rejects>0</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="planar_tor"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>2.6</PDBx:dev_ideal> <PDBx:dev_ideal_target>3.0</PDBx:dev_ideal_target> <PDBx:number>203</PDBx:number> <PDBx:rejects>9</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="staggered_tor"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>17.4</PDBx:dev_ideal> <PDBx:dev_ideal_target>15.0</PDBx:dev_ideal_target> <PDBx:number>298</PDBx:number> <PDBx:rejects>31</PDBx:rejects> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr pdbx_refine_id="X-RAY DIFFRACTION" type="orthonormal_tor"> <PDBx:criterion>&gt; 2\s</PDBx:criterion> <PDBx:dev_ideal>18.1</PDBx:dev_ideal> <PDBx:dev_ideal_target>20.0</PDBx:dev_ideal_target> <PDBx:number>12</PDBx:number> <PDBx:rejects>1</PDBx:rejects> </PDBx:refine_ls_restr> </PDBx:refine_ls_restrCategory> A criterion used to define a parameter value that deviates significantly from its ideal value in the model obtained by restrained least-squares refinement. > 3\s For the given parameter type, the root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. For instance, bond distances may deviate by 0.018 \%A (r.m.s.) from ideal values in the current model. For the given parameter type, the target root-mean-square deviation between the ideal values used as restraints in the least-squares refinement and the values obtained by refinement. The number of parameters of this type subjected to restraint in least-squares refinement. The functional form of the restraint function used in the least-squares refinement. SINUSOIDAL HARMONIC SEMIHARMONIC The number of parameters of this type that deviate from ideal values by more than the amount defined in attribute criterion in category refine_ls_restr in the model obtained by restrained least-squares refinement. The weighting value applied to this type of restraint in the least-squares refinement. This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_ls_restr can be used to distinguish the results of joint refinements. The type of the parameter being restrained. Explicit sets of data values are provided for the programs PROTIN/PROLSQ (beginning with p_) and RESTRAIN (beginning with RESTRAIN_). As computer programs change, these data values are given as examples, not as an enumeration list. Computer programs that convert a data block to a refinement table will expect the exact form of the data values given here to be used. bond distance p_bond_d bond angle expressed as a distance p_angle_d planar 1,4 distance p_planar_d X-H bond distance p_xhbond_d X-H bond angle expressed as a distance p_xhangle_d hydrogen distance p_hydrog_d special distance p_special_d planes p_planar chiral centres p_chiral single-torsion non-bonded contact p_singtor_nbd multiple-torsion non-bonded contact p_multtor_nbd possible (X...Y) hydrogen bond p_xyhbond_nbd possible (X-H...Y) hydrogen bond p_xhyhbond_nbd special torsion angle p_special_tor planar torsion angle p_planar_tor staggered torsion angle p_staggered_tor orthonormal torsion angle p_orthonormal_tor main-chain bond isotropic displacement parameter p_mcbond_it main-chain angle isotropic displacement parameter p_mcangle_it side-chain bond isotropic displacement parameter p_scbond_it side-chain angle isotropic displacement parameter p_scangle_it X-H bond isotropic displacement parameter p_xhbond_it X-H angle isotropic displacement parameter p_xhangle_it special isotropic displacement parameter p_special_it The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range less than 2.12 Angstroms. RESTRAIN_Distances < 2.12 The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range 2.12 - 2.625 Angstroms. RESTRAIN_Distances 2.12 < D < 2.625 The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves in the distance range greater than 2.625 Angstroms. RESTRAIN_Distances > 2.625 The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for peptide planes. RESTRAIN_Peptide Planes The root-mean-square deviation of the difference between the values calculated from the structures used to compile the restraints dictionary parameters and the dictionary values themselves for rings and planes other than peptide planes. RESTRAIN_Ring and other planes RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4 RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6 RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0 RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2 RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4 RESTRAIN_rms diffs for Uiso atoms at dist >2.4 Data items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the end of the refinement. It is expected that these values will only be reported once for each set of restrained domains. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <PDBx:refine_ls_restr_ncsCategory> <PDBx:refine_ls_restr_ncs pdbx_ordinal="1"> <PDBx:dom_id>d2</PDBx:dom_id> <PDBx:ncs_model_details> NCS restraint for pseudo-twofold symmetry between domains d1 and d2. Position weight coefficient given in Kcal/(mol \&#37;A^2^) and isotropic B weight coefficient given in \&#37;A^2^.</PDBx:ncs_model_details> <PDBx:pdbx_asym_id>A</PDBx:pdbx_asym_id> <PDBx:pdbx_ens_id>1</PDBx:pdbx_ens_id> <PDBx:pdbx_refine_id>X-RAY DIFFRACTION</PDBx:pdbx_refine_id> <PDBx:pdbx_type>medium positional</PDBx:pdbx_type> <PDBx:rms_dev_B_iso>0.16</PDBx:rms_dev_B_iso> <PDBx:rms_dev_position>0.09</PDBx:rms_dev_position> <PDBx:weight_B_iso>2.0</PDBx:weight_B_iso> <PDBx:weight_position>300.0</PDBx:weight_position> </PDBx:refine_ls_restr_ncs> </PDBx:refine_ls_restr_ncsCategory> This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. Special aspects of the manner in which noncrystallographic restraints were applied to atomic parameters in the domain specified by attribute dom_id in category refine_ls_restr_ncs and equivalent atomic parameters in the domains against which it was restrained. A reference to attribute id in category struct_asym. A reference to the PDB Chain ID This is a unique identifier for a collection NCS related domains. This references item '_struct_ncs_dom.pdbx_ens_id'. Records the number restraints in the contributing to the RMS statistic. This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_ls_restr_ncs can be used to distinguish the results of joint refinements. Records the standard deviation in the restraint between NCS related domains. The type of NCS restraint. (for example: tight positional) Records the weight used for NCS restraint. The root-mean-square deviation in equivalent isotropic displacement parameters in the domain specified by attribute dom_id in category refine_ls_restr_ncs and in the domains against which it was restrained. The root-mean-square deviation in equivalent atom positions in the domain specified by attribute dom_id in category refine_ls_restr_ncs and in the domains against which it was restrained. The value of the weighting coefficient used in noncrystallographic symmetry restraint of isotropic displacement parameters in the domain specified by attribute dom_id in category refine_ls_restr_ncs to equivalent isotropic displacement parameters in the domains against which it was restrained. The value of the weighting coefficient used in noncrystallographic symmetry restraint of atom positions in the domain specified by attribute dom_id in category refine_ls_restr_ncs to equivalent atom positions in the domains against which it was restrained. An ordinal index for the list of NCS restraints. Data items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement. Example 1 - based on RESTRAIN refinement for the CCP4 test data set toxd. <PDBx:refine_ls_restrCategory> <PDBx:refine_ls_restr type="RESTRAIN_Distances &lt; 2.12"> <PDBx:dev_ideal>0.005</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.022</PDBx:dev_ideal_target> <PDBx:number>509</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_Distances 2.12 &lt; D &lt; 2.625"> <PDBx:dev_ideal>0.016</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.037</PDBx:dev_ideal_target> <PDBx:number>671</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_Distances &gt; 2.625"> <PDBx:dev_ideal>0.034</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.043</PDBx:dev_ideal_target> <PDBx:number>39</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_Peptide Planes"> <PDBx:dev_ideal>0.002</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.010</PDBx:dev_ideal_target> <PDBx:number>59</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_Ring and other planes"> <PDBx:dev_ideal>0.014</PDBx:dev_ideal> <PDBx:dev_ideal_target>0.010</PDBx:dev_ideal_target> <PDBx:number>26</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4"> <PDBx:dev_ideal>0.106</PDBx:dev_ideal> <PDBx:dev_ideal_target xsi:nil="true" /> <PDBx:number>212</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6"> <PDBx:dev_ideal>0.101</PDBx:dev_ideal> <PDBx:dev_ideal_target xsi:nil="true" /> <PDBx:number>288</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0"> <PDBx:dev_ideal>0.077</PDBx:dev_ideal> <PDBx:dev_ideal_target xsi:nil="true" /> <PDBx:number>6</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2"> <PDBx:dev_ideal>0.114</PDBx:dev_ideal> <PDBx:dev_ideal_target xsi:nil="true" /> <PDBx:number>10</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4"> <PDBx:dev_ideal>0.119</PDBx:dev_ideal> <PDBx:dev_ideal_target xsi:nil="true" /> <PDBx:number>215</PDBx:number> </PDBx:refine_ls_restr> <PDBx:refine_ls_restr type="RESTRAIN_rms diffs for Uiso atoms at dist &gt;2.4"> <PDBx:dev_ideal>0.106</PDBx:dev_ideal> <PDBx:dev_ideal_target xsi:nil="true" /> <PDBx:number>461</PDBx:number> </PDBx:refine_ls_restr> </PDBx:refine_ls_restrCategory> <PDBx:refine_ls_restr_typeCategory> <PDBx:refine_ls_restr_type type="RESTRAIN_Distances &lt; 2.12"> <PDBx:distance_cutoff_high>2.12</PDBx:distance_cutoff_high> <PDBx:distance_cutoff_low xsi:nil="true" /> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_Distances 2.12 &lt; D &lt; 2.625"> <PDBx:distance_cutoff_high>2.625</PDBx:distance_cutoff_high> <PDBx:distance_cutoff_low>2.12</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_Distances &gt; 2.625"> <PDBx:distance_cutoff_high xsi:nil="true" /> <PDBx:distance_cutoff_low>2.625</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_Peptide Planes"> <PDBx:distance_cutoff_high xsi:nil="true" /> <PDBx:distance_cutoff_low xsi:nil="true" /> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_Ring and other planes"> <PDBx:distance_cutoff_high xsi:nil="true" /> <PDBx:distance_cutoff_low xsi:nil="true" /> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.2-1.4"> <PDBx:distance_cutoff_high>1.4</PDBx:distance_cutoff_high> <PDBx:distance_cutoff_low>1.2</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.4-1.6"> <PDBx:distance_cutoff_high>1.6</PDBx:distance_cutoff_high> <PDBx:distance_cutoff_low>1.4</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 1.8-2.0"> <PDBx:distance_cutoff_high>2.0</PDBx:distance_cutoff_high> <PDBx:distance_cutoff_low>1.8</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 2.0-2.2"> <PDBx:distance_cutoff_high>2.2</PDBx:distance_cutoff_high> <PDBx:distance_cutoff_low>2.0</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist 2.2-2.4"> <PDBx:distance_cutoff_high>2.4</PDBx:distance_cutoff_high> <PDBx:distance_cutoff_low>2.2</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> <PDBx:refine_ls_restr_type type="RESTRAIN_rms diffs for Uiso atoms at dist &gt;2.4"> <PDBx:distance_cutoff_high xsi:nil="true" /> <PDBx:distance_cutoff_low>2.4</PDBx:distance_cutoff_low> </PDBx:refine_ls_restr_type> </PDBx:refine_ls_restr_typeCategory> The upper limit in angstroms of the distance range applied to the current restraint type. The lower limit in angstroms of the distance range applied to the current restraint type. This data item is a pointer to attribute type in category refine_ls_restr in the REFINE_LS_RESTR category. Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:refine_ls_shellCategory> <PDBx:refine_ls_shell d_res_high="4.51" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:R_factor_obs>0.196</PDBx:R_factor_obs> <PDBx:d_res_low>8.00</PDBx:d_res_low> <PDBx:number_reflns_obs>1226</PDBx:number_reflns_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_high="3.48" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:R_factor_obs>0.146</PDBx:R_factor_obs> <PDBx:d_res_low>4.51</PDBx:d_res_low> <PDBx:number_reflns_obs>1679</PDBx:number_reflns_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_high="2.94" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:R_factor_obs>0.160</PDBx:R_factor_obs> <PDBx:d_res_low>3.48</PDBx:d_res_low> <PDBx:number_reflns_obs>2014</PDBx:number_reflns_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_high="2.59" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:R_factor_obs>0.182</PDBx:R_factor_obs> <PDBx:d_res_low>2.94</PDBx:d_res_low> <PDBx:number_reflns_obs>2147</PDBx:number_reflns_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_high="2.34" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:R_factor_obs>0.193</PDBx:R_factor_obs> <PDBx:d_res_low>2.59</PDBx:d_res_low> <PDBx:number_reflns_obs>2127</PDBx:number_reflns_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_high="2.15" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:R_factor_obs>0.203</PDBx:R_factor_obs> <PDBx:d_res_low>2.34</PDBx:d_res_low> <PDBx:number_reflns_obs>2061</PDBx:number_reflns_obs> </PDBx:refine_ls_shell> <PDBx:refine_ls_shell d_res_high="2.00" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:R_factor_obs>0.188</PDBx:R_factor_obs> <PDBx:d_res_low>2.15</PDBx:d_res_low> <PDBx:number_reflns_obs>1647</PDBx:number_reflns_obs> </PDBx:refine_ls_shell> </PDBx:refine_ls_shellCategory> Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections The estimated error in attribute R_factor_R_free. in category refine_ls_shell The method used to estimate the error is described in the item attribute ls_R_factor_R_free_error_details in category refine. Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low. in category refine_ls_shell sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections Residual factor R for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion. in category reflns sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details in category reflns. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion in category reflns. The crystallographic reliability index Rcomplete for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns Ref: Luebben, J., Gruene, T., (2015). Proc.Nat.Acad.Sci. 112(29) 8999-9003 Fourier Shell Correlation (FSC) between model and observed structure factors for reflections not included in refinement. FSC is a measure of the agreement between observed and calculated structure factors as complex numbers. (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~free~ = -------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation is carried over all free reflections in the resolution shell. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). Fourier Shell Correlation (FSC) between model and observed structure factors for reflections included in refinement. FSC is a measure of the agreement between observed and calculated structure factors as complex numbers. (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~work~ = -------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation is carried over all working reflections in the resolution shell. Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6). The average phase error for all reflections in the resolution shell. 0.30 Total number of bins used. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the reflection limits. The number of reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion in category reflns, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits. The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits. The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by attribute observed_criterion in category reflns to the number of crystallographically unique reflections that satisfy the same limits. Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation limit established by attribute observed_criterion in category reflns, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in attribute R_free_details. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low. in category refine_ls_shell ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections Weighted residual factor wR for reflections that satisfy the resolution limits established by attribute d_res_high in category refine_ls_shell and attribute d_res_low in category refine_ls_shell and the observation criterion established by attribute observed_criterion. in category reflns ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y~calc~ = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight sum is taken over the specified reflections The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution. This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_ls_shell can be used to distinguish the results of joint refinements. Data items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:refine_occupancyCategory> <PDBx:refine_occupancy class="protein" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:details xsi:nil="true" /> <PDBx:treatment>fix</PDBx:treatment> <PDBx:value>1.00</PDBx:value> </PDBx:refine_occupancy> <PDBx:refine_occupancy class="solvent" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:details xsi:nil="true" /> <PDBx:treatment>fix</PDBx:treatment> <PDBx:value>1.00</PDBx:value> </PDBx:refine_occupancy> <PDBx:refine_occupancy class="inhibitor orientation 1" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:details xsi:nil="true" /> <PDBx:treatment>fix</PDBx:treatment> <PDBx:value>0.65</PDBx:value> </PDBx:refine_occupancy> <PDBx:refine_occupancy class="inhibitor orientation 2" pdbx_refine_id="X-RAY DIFFRACTION"> <PDBx:details> The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation.</PDBx:details> <PDBx:treatment>fix</PDBx:treatment> <PDBx:value>0.35</PDBx:value> </PDBx:refine_occupancy> </PDBx:refine_occupancyCategory> A description of special aspects of the occupancy refinement for a class of atoms described in attribute class in category refine_occupancy. The inhibitor binds to the enzyme in two alternative conformations. The occupancy of each conformation was adjusted so as to result in approximately equal mean thermal factors for the atoms in each conformation. The treatment of occupancies for a class of atoms described in attribute class in category refine_occupancy. The value of occupancy assigned to a class of atoms defined in attribute class in category refine_occupancy. Meaningful only for atoms with fixed occupancy. 1.0 0.41 The class of atoms treated similarly for occupancy refinement. all protein solvent sugar-phosphate backbone This data item uniquely identifies a refinement within an entry. attribute pdbx_refine_id in category refine_occupancy can be used to distinguish the results of joint refinements. Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. Example 1 - based on data set fetod of Todres, Yanovsky, Ermekov & Struchkov [Acta Cryst. (1993), C49, 1352-1354]. <PDBx:reflnCategory> <PDBx:refln index_h="2" index_k="0" index_l="0"> <PDBx:F_squared_calc>85.57</PDBx:F_squared_calc> <PDBx:F_squared_meas>58.90</PDBx:F_squared_meas> <PDBx:F_squared_sigma>1.45</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="3" index_k="0" index_l="0"> <PDBx:F_squared_calc>15718.18</PDBx:F_squared_calc> <PDBx:F_squared_meas>15631.06</PDBx:F_squared_meas> <PDBx:F_squared_sigma>30.40</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="4" index_k="0" index_l="0"> <PDBx:F_squared_calc>55613.11</PDBx:F_squared_calc> <PDBx:F_squared_meas>49840.09</PDBx:F_squared_meas> <PDBx:F_squared_sigma>61.86</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="5" index_k="0" index_l="0"> <PDBx:F_squared_calc>246.85</PDBx:F_squared_calc> <PDBx:F_squared_meas>241.86</PDBx:F_squared_meas> <PDBx:F_squared_sigma>10.02</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="6" index_k="0" index_l="0"> <PDBx:F_squared_calc>82.16</PDBx:F_squared_calc> <PDBx:F_squared_meas>69.97</PDBx:F_squared_meas> <PDBx:F_squared_sigma>1.93</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="7" index_k="0" index_l="0"> <PDBx:F_squared_calc>1133.62</PDBx:F_squared_calc> <PDBx:F_squared_meas>947.79</PDBx:F_squared_meas> <PDBx:F_squared_sigma>11.78</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="8" index_k="0" index_l="0"> <PDBx:F_squared_calc>2558.04</PDBx:F_squared_calc> <PDBx:F_squared_meas>2453.33</PDBx:F_squared_meas> <PDBx:F_squared_sigma>20.44</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="9" index_k="0" index_l="0"> <PDBx:F_squared_calc>283.88</PDBx:F_squared_calc> <PDBx:F_squared_meas>393.66</PDBx:F_squared_meas> <PDBx:F_squared_sigma>7.79</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> <PDBx:refln index_h="10" index_k="0" index_l="0"> <PDBx:F_squared_calc>283.70</PDBx:F_squared_calc> <PDBx:F_squared_meas>171.98</PDBx:F_squared_meas> <PDBx:F_squared_sigma>4.26</PDBx:F_squared_sigma> <PDBx:status>o</PDBx:status> </PDBx:refln> </PDBx:reflnCategory> The calculated value of structure-factor component A in electrons. A = |F|cos(phase) The calculated value of structure-factor component A in arbitrary units. A = |F|cos(phase) The measured value of structure-factor component A in electrons. A = |F|cos(phase) The measured value of structure-factor component A in arbitrary units. A = |F|cos(phase) The calculated value of structure-factor component B in electrons. B = |F|sin(phase) The calculated value of structure-factor component B in arbitrary units. B = |F|sin(phase) The measured value of structure-factor component B in electrons. B = |F|sin(phase) The measured value of structure-factor component B in arbitrary units. B = |F|sin(phase) The calculated value of the structure factor in electrons. The calculated value of the structure factor in arbitrary units. The measured value of the structure factor in electrons. The measured value of the structure factor in arbitrary units. The standard uncertainty (estimated standard deviation) of attribute F_meas in category refln in electrons. The standard uncertainty (estimated standard deviation) of attribute F_meas_au in category refln in arbitrary units. The calculated value of the squared structure factor in electrons squared. The measured value of the squared structure factor in electrons squared. The standard uncertainty (derived from measurement) of the squared structure factor in electrons squared. The code identifying the class to which this reflection has been assigned. This code must match a value of attribute code. in category reflns_class Reflections may be grouped into classes for a variety of purposes. For example, for modulated structures each reflection class may be defined by the number m=sum|m~i~|, where the m~i~ are the integer coefficients that, in addition to h,k,l, index the corresponding diffraction vector in the basis defined for the reciprocal lattice. This data item is a pointer to attribute id in category exptl_crystal in the EXPTL_CRYSTAL category. The d spacing in angstroms for this reflection. This is related to the (sin theta)/lambda value by the expression attribute d_spacing in category refln = 2/(_refln.sint/lambda). The figure of merit m for this reflection. int P~alpha~ exp(i*alpha) dalpha m = -------------------------------- int P~alpha~ dalpha P~a~ = the probability that the phase angle a is correct int is taken over the range alpha = 0 to 2 pi. Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors. The calculated value of the intensity in the same units as attribute intensity_meas in category refln. The measured value of the intensity. The standard uncertainty (derived from measurement) of the intensity in the same units as attribute intensity_meas in category refln. Mean path length in millimetres through the crystal for this reflection. The weighted structure factor amplitude for the mFo-DFc map. The weighted phase for the mFo-DFc map. The weighted structure factor amplitude for the 2mFo-DFc map. The calculated value of the structure factor in arbitrary units reflecting only the contribution of the solvent model. The calculated value of the structure factor in arbitrary units including the contribution of the solvent model. The structure factor F(-h,-k,-l) of the Friedel pair. The standard uncertainty (derived from measurement) of the structure factor F(-h,-k,-l) of the Friedel pair. The structure factor F(h,k,l) of the Friedel pair. The standard uncertainty (derived from measurement) of the structure factor F(h,k,l) of the Friedel pair. The isomorphous Hendrickson-Lattman coefficient A~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. The isomorphous Hendrickson-Lattman coefficient B~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. The isomorphous Hendrickson-Lattman coefficient C~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. The isomorphous Hendrickson-Lattman coefficient D~iso~ for this reflection. Ref: Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143. The intensity of the I(-h,-k,-l) partner of the Friedel pair. The standard uncertainty (derived from measurement) of the intensity I(-h,-k,-l) partner of the Friedel pair. The intensity of the I(h,k,l) partner of the Friedel pair. The standard uncertainty (derived from measurement) of the intensity I(h,k,l) partner of the Friedel pair. The weighted phase for the 2mFo-DFc map. The amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l). The standard deviation of the amplitude difference of the Friedel pair, D(hkl) = F(hkl) - F(-h-k-l). The measured anomalous difference. The standard deviation in the anomalous difference. The cosine of the calculated phase An optional identifier for the diffraction data set containing this reflection. The measured diffraction amplitude for this fiber reflection in arbitrary units. The coordinate position in reciprocal space along the fiber layer line for this reflection. The fiber layer line for this reflection. The calculated structure-factor phase in degrees reflecting only the contribution of the solvent model. The calculated structure-factor phase in degrees including the contribution of the solvent model. The phasing cycle. The R-free flag originally assigned to the reflection. The convention used for labeling the work and test sets differs depending on choice of data processing software and refinement program. The signal value for this reflection as defined by _reflns.pdbx_signal_type and _reflns.pdbx_signal_details as calculated by attribute pdbx_signal_software_id in category reflns. The status of a reflection related to attribute pdbx_signal. in category refln A measured reflection counts as observed if: _refln.pdbx_signal >= _reflns.pdbx_observed_signal_threshold and unobserved if: _refln.pdbx_signal < _reflns.pdbx_observed_signal_threshold An unmeasured but observable reflection is one that has not been measured, but the data processing has determined that it would have been expected to be observed had it been measured. An unmeasured and unobservable reflection is one that the data processing has determined would not have been expected to be observed. In datasets in which attribute pdbx_signal in category refln has been populated, a null (?) value for this item indicates an unmeasured reflection for which it is not known whether it is observable or not. The sine of the calculated phase. The calculated structure-factor phase in degrees. The measured structure-factor phase in degrees. Status of a reflection in the structure-refinement process. This data item is a pointer to attribute group_code in category reflns_scale in the REFLNS_SCALE category. The (sin theta)/lambda value in reciprocal angstroms for this reflection. Classification of a reflection so as to indicate its status with respect to inclusion in the refinement and the calculation of R factors. The symmetry reinforcement factor corresponding to the number of times the reflection indices are generated identically from the space-group symmetry operations. The number of symmetry-equivalent reflections. The equivalent reflections have the same structure-factor magnitudes because of the space-group symmetry and the Friedel relationship. The mean wavelength in angstroms of radiation used to measure this reflection. This is an important parameter for data collected using energy-dispersive detectors or the Laue method. This data item is a pointer to attribute wavelength_id in category diffrn_radiation in the DIFFRN_RADIATION category. Miller index h of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Miller index k of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Miller index l of the reflection. The values of the Miller indices in the REFLN category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group. Example 1 - hypothetical example. <PDBx:refln_sys_absCategory> <PDBx:refln_sys_abs index_h="0" index_k="3" index_l="0"> <PDBx:I>28.32</PDBx:I> <PDBx:I_over_sigmaI>1.23</PDBx:I_over_sigmaI> <PDBx:sigmaI>22.95</PDBx:sigmaI> </PDBx:refln_sys_abs> <PDBx:refln_sys_abs index_h="0" index_k="5" index_l="0"> <PDBx:I>14.11</PDBx:I> <PDBx:I_over_sigmaI>0.86</PDBx:I_over_sigmaI> <PDBx:sigmaI>16.38</PDBx:sigmaI> </PDBx:refln_sys_abs> <PDBx:refln_sys_abs index_h="0" index_k="7" index_l="0"> <PDBx:I>114.81</PDBx:I> <PDBx:I_over_sigmaI>5.67</PDBx:I_over_sigmaI> <PDBx:sigmaI>20.22</PDBx:sigmaI> </PDBx:refln_sys_abs> <PDBx:refln_sys_abs index_h="0" index_k="9" index_l="0"> <PDBx:I>32.99</PDBx:I> <PDBx:I_over_sigmaI>1.35</PDBx:I_over_sigmaI> <PDBx:sigmaI>24.51</PDBx:sigmaI> </PDBx:refln_sys_abs> </PDBx:refln_sys_absCategory> The measured value of the intensity in arbitrary units. The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used to evaluate whether a reflection that should be systematically absent according to the designated space group is in fact absent. The standard uncertainty (estimated standard deviation) of attribute I in category refln_sys_abs in arbitrary units. Miller index h of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Miller index k of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Miller index l of the reflection. The values of the Miller indices in the REFLN_SYS_ABS category must correspond to the cell defined by cell lengths and cell angles in the CELL category. Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:reflnsCategory> <PDBx:reflns pdbx_ordinal="1"> <PDBx:d_resolution_high>2.00</PDBx:d_resolution_high> <PDBx:d_resolution_low>8.00</PDBx:d_resolution_low> <PDBx:data_reduction_details> Merging and scaling based on only those reflections with I &gt; \s(I).</PDBx:data_reduction_details> <PDBx:data_reduction_method> Xengen program scalei. Anomalous pairs were merged. Scaling proceeded in several passes, beginning with 1-parameter fit and ending with 3-parameter fit.</PDBx:data_reduction_method> <PDBx:details>none</PDBx:details> <PDBx:entry_id>5HVP</PDBx:entry_id> <PDBx:limit_h_max>22</PDBx:limit_h_max> <PDBx:limit_h_min>0</PDBx:limit_h_min> <PDBx:limit_k_max>46</PDBx:limit_k_max> <PDBx:limit_k_min>0</PDBx:limit_k_min> <PDBx:limit_l_max>57</PDBx:limit_l_max> <PDBx:limit_l_min>0</PDBx:limit_l_min> <PDBx:number_obs>7228</PDBx:number_obs> <PDBx:observed_criterion>&gt; 1 \s(I)</PDBx:observed_criterion> <PDBx:pdbx_diffrn_id>1</PDBx:pdbx_diffrn_id> </PDBx:reflns> </PDBx:reflnsCategory> Example 2 - based on data set TOZ of Willis, Beckwith & Tozer [Acta Cryst. (1991), C47, 2276-2277]. <PDBx:reflnsCategory> <PDBx:reflns pdbx_ordinal="1"> <PDBx:d_resolution_high>0.8733</PDBx:d_resolution_high> <PDBx:d_resolution_low>11.9202</PDBx:d_resolution_low> <PDBx:entry_id>1TOZ</PDBx:entry_id> <PDBx:limit_h_max>6</PDBx:limit_h_max> <PDBx:limit_h_min>0</PDBx:limit_h_min> <PDBx:limit_k_max>17</PDBx:limit_k_max> <PDBx:limit_k_min>0</PDBx:limit_k_min> <PDBx:limit_l_max>22</PDBx:limit_l_max> <PDBx:limit_l_min>0</PDBx:limit_l_min> <PDBx:number_all>1592</PDBx:number_all> <PDBx:number_obs>1408</PDBx:number_obs> <PDBx:observed_criterion>F_&gt;_6.0_\s(F)</PDBx:observed_criterion> <PDBx:pdbx_diffrn_id>1</PDBx:pdbx_diffrn_id> </PDBx:reflns> </PDBx:reflnsCategory> The value of the overall isotropic displacement parameter estimated from the slope of the Wilson plot. The proportion of Friedel-related reflections present in the number of 'independent' reflections specified by the item attribute number_all. in category reflns This proportion is calculated as the ratio: [N(Crystal class) - N(Laue symmetry)] / N(Laue symmetry) where, working from the DIFFRN_REFLN list, N(Crystal class) is the number of reflections obtained on averaging under the symmetry of the crystal class N(Laue symmetry) is the number of reflections obtained on averaging under the Laue symmetry. Examples: (a) For centrosymmetric structures, the value of attribute Friedel_coverage in category reflns is necessarily equal to 0.0, as the crystal class is identical to the Laue symmetry. (b) For whole-sphere data for a crystal in the space group P1, attribute Friedel_coverage in category reflns is equal to 1.0, as no reflection h k l is equivalent to -h -k -l in the crystal class and all Friedel pairs {h k l; -h -k -l} have been measured. (c) For whole-sphere data in space group Pmm2, attribute Friedel_coverage in category reflns will be < 1.0 because although reflections h k l and -h -k -l are not equivalent when h k l indices are nonzero, they are when l=0. (d) For a crystal in space group Pmm2, measurements of the two inequivalent octants h >= 0, k >=0, l lead to the same value as in (c), whereas measurements of the two equivalent octants h >= 0, k, l >= 0 will lead to a zero value for attribute Friedel_coverage in category reflns. A description of the method by which a subset of reflections was selected for exclusion from refinement so as to be used in the calculation of a 'free' R factor. The data set was sorted with l varying most rapidly and h varying least rapidly. Every 10th reflection in this sorted list was excluded from refinement and included in the calculation of a 'free' R factor. Residual factor Rmerge for all reflections that satisfy the resolution limits established by attribute d_resolution_high in category reflns and attribute d_resolution_low. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection Residual factor Rmerge for reflections that satisfy the resolution limits established by attribute d_resolution_high in category reflns and attribute d_resolution_low in category reflns and the observation limit established by attribute observed_criterion. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The smallest value in angstroms for the interplanar spacings for the reflection data. This is called the highest resolution. The largest value in angstroms for the interplanar spacings for the reflection data. This is called the lowest resolution. A description of special aspects of the data-reduction procedures. Merging and scaling based on only those reflections with I > sig(I). The method used for data reduction. Note that this is not the computer program used, which is described in the SOFTWARE category, but the method itself. This data item should be used to describe significant methodological options used within the data-reduction programs. Profile fitting by method of Kabsch (1987). Scaling used spherical harmonic coefficients. A description of reflection data not covered by other data names. This should include details of the Friedel pairs. This data item is a pointer to attribute id in category entry in the ENTRY category. Maximum value of the Miller index h for the reflection data. This need not have the same value as attribute limit_h_max in category diffrn_reflns. Minimum value of the Miller index h for the reflection data. This need not have the same value as attribute limit_h_min in category diffrn_reflns. Maximum value of the Miller index k for the reflection data. This need not have the same value as attribute limit_k_max in category diffrn_reflns. Minimum value of the Miller index k for the reflection data. This need not have the same value as attribute limit_k_min in category diffrn_reflns. Maximum value of the Miller index l for the reflection data. This need not have the same value as attribute limit_l_max in category diffrn_reflns. Minimum value of the Miller index l for the reflection data. This need not have the same value as attribute limit_l_min in category diffrn_reflns. The total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. The item attribute details in category reflns describes the reflection data. The number of reflections in the REFLN list (not the DIFFRN_REFLN list) that are significantly intense, satisfying the criterion specified by attribute threshold_expression in category reflns. This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item attribute details in category reflns. The number of reflections in the REFLN list (not the DIFFRN_REFLN list) classified as observed (see attribute observed_criterion). in category reflns This number may contain Friedel-equivalent reflections according to the nature of the structure and the procedures used. The criterion used to classify a reflection as 'observed'. This criterion is usually expressed in terms of a sigma(I) or sigma(F) threshold. >2sigma(I) The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of F. The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of F. The criterion used to classify a reflection as 'observed' expressed as an upper limit for the value of I. The criterion used to classify a reflection as 'observed' expressed as a lower limit for the value of I. The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(F). The criterion used to classify a reflection as 'observed' expressed as a multiple of the value of sigma(I). The Pearson's correlation coefficient expressed as a decimal value between the average intensities from randomly selected half-datasets. Ref: Karplus & Diederichs (2012), Science 336, 1030-33 The overall correlation coefficient between two randomly chosen half-sets of anomalous intensity differences, I(+)-I(-) for anomalous data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns, i.e. data for which intensities for both instances of a Friedel pair are available for an acentric reflection. Estimates the value of CC_true, the true correlation coefficient between the average intensities from randomly selected half-datasets. CC_star = sqrt(2*CC_half/(1+CC_half)), where both CC_star and CC_half (CC1/2) Ref: Karplus & Diederichs (2012), Science 336, 1030-33 R split measures the agreement between the sets of intensities created by merging odd- and even-numbered images from the overall data. Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341 The R value for merging all intensities in this data set. This item is the same as attribute pdbx_Rmerge_I in category reflns, but applies only to observed Friedel pairs. The R value for merging intensities satisfying the observed criteria in this data set. The precision-indicating merging R factor value Rpim, for merging all intensities in this data set. sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rpim = -------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. This item is the same as attribute pdbx_Rpim_I_all in category reflns, but applies only to observed Friedel pairs. The redundancy-independent merging R factor value Rrim, also denoted Rmeas, for merging all intensities in this data set. sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rrim = ---------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. This item is the same as attribute pdbx_Rrim_I_all, in category reflns but applies to the observed Friedel pairs only. The R sym value as a decimal number. 0.02 The overall mean ratio of absolute anomalous intensity differences to their standard deviation within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns and using data for which intensities for both instances of a Friedel pair are available for an acentric reflection. |Dano| ------------- sigma(Dano) with Dano = I(+) - I(-) sigma(Dano) = sqrt( sigma(I(+))^2 + sigma(I(-))^2 ) Eigen-B-factor along the first eigenvector of the diffraction anisotropy tensor Eigen-B-factor along the second eigenvector of the diffraction anisotropy tensor Eigen-B-factor along the third eigenvector of the diffraction anisotropy tensor X component of the first eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Y component of the first eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Z component of the first eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. X component of the second eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Y component of the second eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Z component of the second eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. X component of the third eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Y component of the third eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Z component of the third eigenvector of the diffraction anisotropy tensor. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Anisotropic diffraction limit along principal axis 1 (of ellipsoid fitted to the diffraction cut-off surface). Anisotropic diffraction limit along principal axis 2 (of ellipsoid fitted to the diffraction cut-off surface) Anisotropic diffraction limit along principal axis 3 (of ellipsoid fitted to the diffraction cut-off surface) Principal axis 1 (X component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Principal axis 1 (Y component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Principal axis 1 (Z component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Principal axis 2 (X component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Principal axis 2 (Y component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Principal axis 2 (Z component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Principal axis 3 (X component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Principal axis 3 (Y component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Principal axis 3 (Z component) of ellipsoid fitted to the diffraction cut-off surface. The applicable orthogonalization convention is that specified by attribute pdbx_orthogonalization_convention in category reflns. Overall Chi-squared statistic. The optical resolution of the data set, d(opt), is the expected minimum distance between two resolved peaks in an electron-density map. d(opt) = {2[sigma(Patt)2^ + sigma(sph)2^]}1/2^ sigma(Patt) = standard deviation of the Gaussian function fitted to the Patterson origin peak sigma(sph) = standard deviation of the Gaussian function fitted to the origin peak of the spherical interference function, representing the Fourier transform of a sphere with radius 1/dmin dmin = nominal resolution (_reflns.d_resolution_high) Ref: Vaguine, A. A., Richelle, J. & Wodak, S. J. (1999). Acta Cryst. D55, 191-205. (see also http://www.ysbl.york.ac.uk/~alexei/sfcheck.html) Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. The highest optical resolution for this reflection data set as determined by computational method attribute pdbx_d_res_opt_method in category reflns. 1.2 The lowest optical resolution for this reflection data set as determined by computational method attribute pdbx_d_res_opt_method in category reflns. 20.5 The computational method used to determine the optical resolution limits attribute pdbx_d_res_high_opt in category reflns and attribute pdbx_d_res_low_opt in category reflns. SFCHECK An identifier for the diffraction data set for this set of summary statistics. Multiple diffraction data sets entered as a comma separated list. The ratio of the average intensity to the average uncertainty, <I>/<sigma(I)>. The mean of the ratio of the intensities to their standard uncertainties, <I/sigma(I)>. This item is the same as attribute number_obs in category reflns, but applies to observed Friedel pairs only. Total number of measured reflections. 23000 140000 The threshold value for attribute pdbx_signal in category refln as used to define the status of an individual reflection according to the description in attribute pdbx_signal_status in category refln. Description of orthogonalization convention used. The notation can make use of unit cell axes "a", "b" and "c" and the reciprocal unit cell axes "astar", "bstar" and "cstar". Upper case letters "X", "Y" and "Z" denote the orthogonal axes, while lower case "x" stands for "cross product". Completeness (as a percentage) of symmetry-unique anomalous difference data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns relative to all possible symmetry-unique anomalous difference data within that sphere. Completeness (as a percentage) of symmetry-unique data within the intersection of (1) a sphere (defined by the diffraction limits, attribute d_resolution_high in category reflns and attribute d_resolution_low) in category reflns and (2) the ellipsoid (described by attribute pdbx_aniso_diffraction_limit_* in category _reflns items), relative to all possible symmetry-unique reflections within that intersection. Completeness (as a percentage) of symmetry-unique anomalous difference data within the intersection of (1) a sphere (defined by the diffraction limits, _reflns.d_resolution_high and _reflns.d_resolution_low) and (2) the ellipsoid (described by attribute pdbx_aniso_diffraction_limit_* in category _reflns items), relative to all possible symmetry-unique anomalous difference data within that intersection. Completeness (as a percentage) of symmetry-unique data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns relative to all possible symmetry-unique reflections within that sphere. In the absence of an anisotropy description this is identical to attribute percent_possible_obs in category reflns. Completeness (as a percentage) of symmetry-unique anomalous difference data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns relative to all possible symmetry-unique anomalous difference data within that sphere. In the absence of an anisotropy description this is identical to attribute pdbx_percent_possible_anomalous in category reflns. Overall redundancy for this data set. The overall redundancy of anomalous difference data within the sphere defined by the diffraction limits (_reflns.d_resolution_high and attribute d_resolution_low) in category reflns, i.e. data for which intensities for both instances of a Friedel pair are available for an acentric reflection. The redundancy in set of observed reflections. Resolution (angstrom) for reflections with <I>/<sigma(I)> = 2. Resolution (angstroms) for reflections with <I/sigma(I)> = 2. Number of reflections rejected in scaling operations. Further details about the calculation of the values assigned to attribute pdbx_signal in category refln The software used to calculate the values of attribute pdbx_signal in category refln Type of signal used for _reflns.pdbx_observed_signal_threshold and _refln.pdbx_signal In the enumeration details: Imean is the inverse-variance weighted mean intensity of all measurements for a given symmetry-unique reflection Ihalf is the inverse-variance weighted mean intensity of a random half-selection of all measurements for a given symmetry-unique reflection The percentage of geometrically possible reflections represented by reflections that satisfy the resolution limits established by _reflns.d_resolution_high and _reflns.d_resolution_low and the observation limit established by attribute observed_criterion in category reflns. The value of attribute phase_calculation_details in category reflns describes a special details about calculation of phases in attribute phase_calc in category refln. From model NCS averaging Solvent flipping Solvent flattening Multiple crystal averaging Multiple phase modification Other phase modification The threshold, usually based on multiples of u(I), u(F^2^) or u(F), that serves to identify significantly intense reflections, the number of which is given by attribute number_gt. in category reflns These reflections are used in the calculation of attribute ls_R_factor_gt in category refine. I>2u(I) An ordinal identifier for this set of reflection statistics. Data items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class. Example 1 - example corresponding to the one-dimensional incommensurately modulated structure of K~2~SeO~4~. <PDBx:reflns_classCategory> <PDBx:reflns_class code="Main"> <PDBx:number_gt>584</PDBx:number_gt> </PDBx:reflns_class> <PDBx:reflns_class code="Sat1"> <PDBx:number_gt>226</PDBx:number_gt> </PDBx:reflns_class> <PDBx:reflns_class code="Sat2"> <PDBx:number_gt>50</PDBx:number_gt> </PDBx:reflns_class> </PDBx:reflns_classCategory> For each reflection class, the residual factor R(F^2^) calculated on the squared amplitudes of the observed and calculated structure factors for the reflections judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. sum | F(obs)^2^ - F(calc)^2^ | R(Fsqd) = ------------------------------- sum F(obs)^2^ F(obs)^2^ = squares of the observed structure-factor amplitudes F(calc)^2^ = squares of the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. For each reflection class, the residual factor R(I) for the reflections judged significantly intense (i.e. satisfying the threshold specified by attribute threshold_expression) in category reflns and included in the refinement. This is most often calculated in Rietveld refinements against powder data, where it is referred to as R~B~ or R~Bragg~. sum | I(obs) - I(calc) | R(I) = ------------------------ sum | I(obs) | I(obs) = the net observed intensities I(calc) = the net calculated intensities and the sum is taken over the reflections of this class. For each reflection class, the residual factor for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of attribute wR_factor_all. in category reflns_class sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. For each reflection class, the residual factor for significantly intense reflections (see attribute threshold_expression) in category reflns included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. This is the conventional R factor. See also the definition of attribute wR_factor_all. in category reflns_class sum | F(obs) - F(calc) | R = ------------------------ sum | F(obs) | F(obs) = the observed structure-factor amplitudes F(calc) = the calculated structure-factor amplitudes and the sum is taken over the reflections of this class. For each reflection class, the smallest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the highest resolution. For each reflection class, the largest value in angstroms for the interplanar spacings for the reflections used in the refinement. This is called the lowest resolution. Description of each reflection class. m=1 first order satellites H0L0 common projection reflections For each reflection class, the number of significantly intense reflections (see attribute threshold_expression) in category reflns in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel- equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item attribute details in category reflns. For each reflection class, the total number of reflections in the REFLN list (not the DIFFRN_REFLN list). This may include Friedel-equivalent reflections (i.e. those which are symmetry-equivalent under the Laue symmetry but inequivalent under the crystal class) according to the nature of the structure and the procedures used. Any special characteristics of the reflections included in the REFLN list should be described using the item attribute details in category reflns. For each reflection class, the weighted residual factors for all reflections included in the refinement. The reflections also satisfy the resolution limits established by _reflns_class.d_res_high and _reflns_class.d_res_low. See also attribute R_factor_ in category reflns_class definitions. ( sum w [ Y(obs) - Y(calc) ]^2^ )^1/2^ wR = ( ------------------------------ ) ( sum w Y(obs)^2^ ) Y(obs) = the observed amplitude specified by attribute ls_structure_factor_coef in category refine Y(calc) = the calculated amplitude specified by attribute ls_structure_factor_coef in category refine w = the least-squares weight and the sum is taken over the reflections of this class. The code identifying a certain reflection class. 1 m1 s2 Data items in the REFLNS_SCALE category record details about the structure-factor scales. They are referenced from within the REFLN list through attribute scale_group_code in category refln. Example 1 - based on laboratory records for the collagen-like peptide [(POG)4 EKG (POG)5]3. <PDBx:reflns_scaleCategory> <PDBx:reflns_scale group_code="SG1"> <PDBx:meas_F>4.0</PDBx:meas_F> </PDBx:reflns_scale> </PDBx:reflns_scaleCategory> A scale associated with attribute group_code in category reflns_scale. A scale associated with attribute group_code in category reflns_scale. A scale associated with attribute group_code in category reflns_scale. The code identifying a scale attribute meas_F, in category reflns_scale _reflns_scale.meas_F_squared or _reflns_scale.meas_intensity. These are linked to the REFLN list by the attribute scale_group_code in category refln. These codes need not correspond to those in the DIFFRN_SCALE list. 1 2 c1 c2 Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:reflns_shellCategory> <PDBx:reflns_shell pdbx_ordinal="1"> <PDBx:Rmerge_F_obs>1.98</PDBx:Rmerge_F_obs> <PDBx:d_res_high>31.38</PDBx:d_res_high> <PDBx:d_res_low>3.82</PDBx:d_res_low> <PDBx:meanI_over_sigI_obs>69.8</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>9024</PDBx:number_measured_obs> <PDBx:number_unique_obs>2540</PDBx:number_unique_obs> <PDBx:percent_possible_obs>96.8</PDBx:percent_possible_obs> </PDBx:reflns_shell> <PDBx:reflns_shell pdbx_ordinal="2"> <PDBx:Rmerge_F_obs>3.85</PDBx:Rmerge_F_obs> <PDBx:d_res_high>3.82</PDBx:d_res_high> <PDBx:d_res_low>3.03</PDBx:d_res_low> <PDBx:meanI_over_sigI_obs>26.1</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>7413</PDBx:number_measured_obs> <PDBx:number_unique_obs>2364</PDBx:number_unique_obs> <PDBx:percent_possible_obs>95.1</PDBx:percent_possible_obs> </PDBx:reflns_shell> <PDBx:reflns_shell pdbx_ordinal="3"> <PDBx:Rmerge_F_obs>6.37</PDBx:Rmerge_F_obs> <PDBx:d_res_high>3.03</PDBx:d_res_high> <PDBx:d_res_low>2.65</PDBx:d_res_low> <PDBx:meanI_over_sigI_obs>10.5</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>5640</PDBx:number_measured_obs> <PDBx:number_unique_obs>2123</PDBx:number_unique_obs> <PDBx:percent_possible_obs>86.2</PDBx:percent_possible_obs> </PDBx:reflns_shell> <PDBx:reflns_shell pdbx_ordinal="4"> <PDBx:Rmerge_F_obs>8.01</PDBx:Rmerge_F_obs> <PDBx:d_res_high>2.65</PDBx:d_res_high> <PDBx:d_res_low>2.41</PDBx:d_res_low> <PDBx:meanI_over_sigI_obs>6.4</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>4322</PDBx:number_measured_obs> <PDBx:number_unique_obs>1882</PDBx:number_unique_obs> <PDBx:percent_possible_obs>76.8</PDBx:percent_possible_obs> </PDBx:reflns_shell> <PDBx:reflns_shell pdbx_ordinal="5"> <PDBx:Rmerge_F_obs>9.86</PDBx:Rmerge_F_obs> <PDBx:d_res_high>2.41</PDBx:d_res_high> <PDBx:d_res_low>2.23</PDBx:d_res_low> <PDBx:meanI_over_sigI_obs>4.3</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>3247</PDBx:number_measured_obs> <PDBx:number_unique_obs>1714</PDBx:number_unique_obs> <PDBx:percent_possible_obs>70.4</PDBx:percent_possible_obs> </PDBx:reflns_shell> <PDBx:reflns_shell pdbx_ordinal="6"> <PDBx:Rmerge_F_obs>13.99</PDBx:Rmerge_F_obs> <PDBx:d_res_high>2.23</PDBx:d_res_high> <PDBx:d_res_low>2.10</PDBx:d_res_low> <PDBx:meanI_over_sigI_obs>3.1</PDBx:meanI_over_sigI_obs> <PDBx:number_measured_obs>1140</PDBx:number_measured_obs> <PDBx:number_unique_obs>812</PDBx:number_unique_obs> <PDBx:percent_possible_obs>33.3</PDBx:percent_possible_obs> </PDBx:reflns_shell> </PDBx:reflns_shellCategory> Residual factor Rmerge for all reflections that satisfy the resolution limits established by attribute d_res_high in category reflns_shell and attribute d_res_low. in category reflns_shell sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The value of Rmerge(F) for significantly intense reflections (see attribute threshold_expression) in category reflns in a given shell. sum~i~ ( sum~j~ | F~j~ - <F> | ) Rmerge(F) = -------------------------------- sum~i~ ( sum~j~ <F> ) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Residual factor Rmerge for reflections that satisfy the resolution limits established by attribute d_res_high in category reflns_shell and attribute d_res_low in category reflns_shell and the observation criterion established by attribute observed_criterion. in category reflns sum~i~(sum~j~|F~j~ - <F>|) Rmerge(F) = -------------------------- sum~i~(sum~j~<F>) F~j~ = the amplitude of the jth observation of reflection i <F> = the mean of the amplitudes of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The value of Rmerge(I) for all reflections in a given shell. sum~i~(sum~j~|I~j~ - <I>|) Rmerge(I) = -------------------------- sum~i~(sum~j~<I>) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The value of Rmerge(I) for significantly intense reflections (see attribute threshold_expression) in category reflns in a given shell. sum~i~ ( sum~j~ | I~j~ - <I> | ) Rmerge(I) = -------------------------------- sum~i~ ( sum~j~ <I> ) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. The value of Rmerge(I) for reflections classified as 'observed' (see attribute observed_criterion) in category reflns in a given shell. sum~i~(sum~j~|I~j~ - <I>|) Rmerge(I) = -------------------------- sum~i~(sum~j~<I>) I~j~ = the intensity of the jth observation of reflection i <I> = the mean of the intensities of all observations of reflection i sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection The smallest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the highest resolution. The highest value in angstroms for the interplanar spacings for the reflections in this shell. This is called the lowest resolution. The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. The ratio of the mean of the intensities of the significantly intense reflections (see attribute threshold_expression) in category reflns in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell. The ratio of the mean of the intensities of the reflections classified as 'observed' (see attribute observed_criterion) in category reflns in this shell to the mean of the standard uncertainties of the intensities of the 'observed' reflections in this shell. The ratio of the mean of the intensities of all reflections in this shell to the mean of the standard uncertainties of the intensities of all reflections in this shell. The ratio of the mean of the intensities of the significantly intense reflections (see attribute threshold_expression) in category reflns in this shell to the mean of the standard uncertainties of the intensities of the significantly intense reflections in this shell. The total number of reflections measured for this shell. The number of significantly intense reflections (see attribute threshold_expression) in category reflns measured for this shell. The number of reflections classified as 'observed' (see attribute observed_criterion) in category reflns for this shell. The number of unique reflections it is possible to measure in this shell. The total number of measured reflections which are symmetry- unique after merging for this shell. The total number of significantly intense reflections (see attribute threshold_expression) in category reflns resulting from merging measured symmetry-equivalent reflections for this resolution shell. The total number of measured reflections classified as 'observed' (see attribute observed_criterion) in category reflns which are symmetry-unique after merging for this shell. The Pearson's correlation coefficient expressed as a decimal value between the average intensities from randomly selected half-datasets within the resolution shell. Ref: Karplus & Diederichs (2012), Science 336, 1030-33 The correlation coefficient within the spherical shell (defined by its diffraction limits attribute d_resolution_high in category reflns_shell and attribute d_resolution_low) in category reflns_shell between two randomly chosen half-sets of anomalous intensity differences, I(+)-I(-) for anomalous data, i.e. data for which intensities for both instances of a Friedel pair are available for an acentric reflection. Estimates the value of CC_true, the true correlation coefficient between the average intensities from randomly selected half-datasets within the resolution shell. CC_star = sqrt(2*CC_half/(1+CC_half)) Ref: Karplus & Diederichs (2012), Science 336, 1030-33 R split measures the agreement between the sets of intensities created by merging odd- and even-numbered images from the data within the resolution shell. Ref: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman (2012), J. Appl. Cryst. 45, 335-341 This item is the same as attribute pdbx_Rmerge_I_all in category reflns_shell, but applies to observed Friedel pairs only. The precision-indicating merging R factor value Rpim, for merging all intensities in a given shell. sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rpim = -------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. This item serves the same purpose as attribute pdbx_Rpim_I_all in category reflns_shell, but applies to observed Friedel pairs only. The redundancy-independent merging R factor value Rrim, also denoted Rmeas, for merging all intensities in a given shell. sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> | Rrim = -------------------------------------------------------- sum~i~ ( sum~j~ I~j~ ) I~j~ = the intensity of the jth observation of reflection i <I~i~> = the mean of the intensities of all observations of reflection i N~i~ = the redundancy (the number of times reflection i has been measured). sum~i~ is taken over all reflections sum~j~ is taken over all observations of each reflection. Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct. Biol. 4, 269-275. Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst. 30, 203-205. Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135. This item is the duplicate of attribute pdbx_Rrim_I_all in category reflns_shell, but is limited to observed Friedel pairs. R sym value in percent. The mean ratio of absolute anomalous intensity differences to their standard deviation within the spherical shell (defined by its diffraction limits attribute d_resolution_high in category reflns_shell and attribute d_resolution_low). in category reflns_shell |Dano| ------------- sigma(Dano) with Dano = I(+) - I(-) sigma(Dano) = sqrt( sigma(I(+))^2 + sigma(I(-))^2 ) Chi-squared statistic for this resolution shell. An identifier for the diffraction data set corresponding to this resolution shell. Multiple diffraction data sets specified as a comma separated list. The mean of the ratio of the intensities to their standard uncertainties of all reflections in the resolution shell. attribute pdbx_netI_over_sigmaI_all in category reflns_shell = <I/sigma(I)> The mean of the ratio of the intensities to their standard uncertainties of observed reflections (see attribute observed_criterion) in category reflns in the resolution shell. attribute pdbx_netI_over_sigmaI_obs in category reflns_shell = <I/sigma(I)> This item is a duplicate of attribute number_unique_all, in category reflns_shell but only for the observed Friedel pairs. Completeness (as a percentage) of symmetry-unique anomalous difference data within the spherical shell defined by its diffraction limits (_reflns_shell.d_resolution_high and attribute d_resolution_low) in category reflns_shell relative to all possible symmetry-unique anomalous difference data within that shell. Completeness (as a percentage) of symmetry-unique data within the intersection of (1) a spherical shell (defined by its diffraction limits, attribute d_resolution_high in category reflns_shell and attribute d_resolution_low) in category reflns_shell and (2) the ellipsoid (described by attribute pdbx_aniso_diffraction_limit_* in category _reflns items), relative to all possible symmetry-unique reflections within that intersection. Completeness (as a percentage) of symmetry-unique anomalous difference data within the intersection of (1) a spherical shell (defined by its diffraction limits, attribute d_resolution_high in category reflns_shell and attribute d_resolution_low) in category reflns_shell and (2) the ellipsoid (described by attribute pdbx_aniso_diffraction_limit_* in category _reflns items), relative to all possible symmetry-unique anomalous difference data within that intersection. Completeness (as a percentage) of symmetry-unique data within the spherical shell defined by its diffraction limits (_reflns_shell.d_resolution_high and attribute d_resolution_low) in category reflns_shell relative to all possible symmetry-unique reflections within that shell. In the absence of an anisotropy description this is identical to attribute percent_possible_all in category reflns_shell. Completeness (as a percentage) of symmetry-unique anomalous difference data within the spherical shell defined by its diffraction limits (_reflns_shell.d_resolution_high and attribute d_resolution_low) in category reflns_shell relative to all possible symmetry-unique anomalous difference data within that shell. In the absence of an anisotropy description this is identical to attribute pdbx_percent_possible_anomalous in category reflns. Redundancy for the current shell. The redundancy of anomalous difference data within the spherical shell (defined by its diffraction limits attribute d_resolution_high in category reflns_shell and attribute d_resolution_low) in category reflns_shell, i.e. data for which intensities for both instances of a Friedel pair are available for an acentric reflection. For this shell, the redundancy in the observed reflections. 3.1 The number of rejected reflections in the resolution shell. Reflections may be rejected from scaling by setting the observation criterion, attribute observed_criterion. in category reflns The percentage of geometrically possible reflections represented by all reflections measured for this shell. The percentage of geometrically possible reflections represented by significantly intense reflections (see attribute threshold_expression) in category reflns measured for this shell. The percentage of geometrically possible reflections represented by reflections classified as 'observed' (see attribute observed_criterion) in category reflns for this shell. An ordinal identifier for this resolution shell. Data items in the SOFTWARE category record details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation. These data items allow computer programs to be referenced in more detail than data items in the COMPUTING category do. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:softwareCategory> <PDBx:software pdbx_ordinal="1"> <PDBx:citation_id>ref5</PDBx:citation_id> <PDBx:classification>refinement</PDBx:classification> <PDBx:compiler_name>Convex Fortran</PDBx:compiler_name> <PDBx:compiler_version>v8.0</PDBx:compiler_version> <PDBx:contact_author>Wayne A. Hendrickson</PDBx:contact_author> <PDBx:date xsi:nil="true" /> <PDBx:dependencies>Requires that Protin be run first</PDBx:dependencies> <PDBx:description>restrained least-squares refinement</PDBx:description> <PDBx:hardware>Convex C220</PDBx:hardware> <PDBx:language>Fortran</PDBx:language> <PDBx:location>ftp://rosebud.sdsc.edu/pub/sdsc/xtal/CCP4/ccp4/</PDBx:location> <PDBx:mods>optimized</PDBx:mods> <PDBx:name>Prolsq</PDBx:name> <PDBx:os>ConvexOS</PDBx:os> <PDBx:os_version>v10.1</PDBx:os_version> <PDBx:type>program</PDBx:type> <PDBx:version>unknown</PDBx:version> </PDBx:software> </PDBx:softwareCategory> This data item is a pointer to attribute id in category citation in the CITATION category. The classification of the program according to its major function. data collection data reduction phasing model building refinement validation other The compiler used to compile the software. Convex Fortran gcc DEC C The version of the compiler used to compile the software. 3.1 2.1 alpha The recognized contact author of the software. This could be the original author, someone who has modified the code or someone who maintains the code. It should be the person most commonly associated with the code. T. Alwyn Jones Axel Brunger The e-mail address of the person specified in attribute contact_author in category software. bourne@sdsc.edu The date the software was released. 1991-10-01 1990-04-30 Any prerequisite software required to run attribute name in category software. PDBlib class library Description of the software. Uses method of restrained least squares The hardware upon which the software was run. Sun Sparc 10 model 41 Dec Alpha 3000 model 500S Silicon Graphics Elan Compaq PC 486/66 The major computing language in which the software is coded. The URL for an Internet address at which details of the software can be found. http://rosebud.sdsc.edu/projects/pb/IUCr/software.html ftp://ftp.sdsc.edu/pub/sdsc/biology/ Any noteworthy modifications to the base software, if applicable. Added support for space group F432 The name of the software. Merlot O Xengen X-plor The name of the operating system under which the software runs. Ultrix OpenVMS DOS Windows 95 Windows NT Irix HPUX DEC Unix The version of the operating system under which the software runs. 3.1 4.2.1 The classification of the software according to the most common types. The version of the software. v1.0 beta 3.1-2 unknown An ordinal index for this category 1 2 Contains all the data items that refer to the space group as a whole, such as its name or crystal system. They may be looped, for example, in a list of space groups and their properties. Only a subset of the SPACE_GROUP category items appear in this dictionary. The remainder are found in the symmetry CIF dictionary. Space-group types are identified by their number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary. Example 1 - the monoclinic space group No. 15 with unique axis b. <PDBx:space_groupCategory> <PDBx:space_group id="1"> <PDBx:IT_number>15</PDBx:IT_number> <PDBx:crystal_system>monoclinic</PDBx:crystal_system> <PDBx:name_H-M_alt>C 2/c</PDBx:name_H-M_alt> <PDBx:name_Hall>-C 2yc</PDBx:name_Hall> </PDBx:space_group> </PDBx:space_groupCategory> The number as assigned in International Tables for Crystallography Vol. A, specifying the proper affine class (i.e. the orientation-preserving affine class) of space groups (crystallographic space-group type) to which the space group belongs. This number defines the space-group type but not the coordinate system in which it is expressed. The name of the system of geometric crystal classes of space groups (crystal system) to which the space group belongs. Note that rhombohedral space groups belong to the trigonal system. attribute name_H-M_alt in category space_group allows any Hermann-Mauguin symbol to be given. The way in which this item is used is determined by the user and in general is not intended to be interpreted by computer. It may, for example, be used to give one of the extended Hermann-Mauguin symbols given in Table 4.3.2.1 of International Tables for Crystallography Vol. A (2002) or a Hermann-Mauguin symbol for a conventional or unconventional setting. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. Subscripts should appear without special symbols. Bars should be given as negative signs before the numbers to which they apply. The commonly used Hermann-Mauguin symbol determines the space- group type uniquely but a given space-group type may be described by more than one Hermann-Mauguin symbol. The space- group type is best described using attribute IT_number. in category space_group The Hermann-Mauguin symbol may contain information on the choice of basis, but not on the choice of origin. To define the setting uniquely, use attribute name_Hall in category space_group or list the symmetry operations. three examples for space group No. 63 loop_ _space_group.name_H-M_alt 'C m c m' 'C 2/c 2/m 21/m' 'A m a m' Space-group symbol defined by Hall. Each component of the space-group name is separated by a space or an underscore. The use of a space is strongly recommended. The underscore is only retained because it was used in old CIFs. It should not be used in new CIFs. attribute name_Hall in category space_group uniquely defines the space group and its reference to a particular coordinate system. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981), A37, 921. [See also International Tables for Crystallography Vol. B (2001), Chapter 1.4, Appendix 1.4.2.] equivalent to Pca21 P 2c -2ac equivalent to Ia3d -I 4bd 2ab 3 This is the unique identifier for the SPACE_GROUP category. Contains information about the symmetry operations of the space group. Example 1 - The symmetry operations for the space group P21/c. <PDBx:space_group_symopCategory> <PDBx:space_group_symop id="1"> <PDBx:operation_xyz>x,y,z</PDBx:operation_xyz> </PDBx:space_group_symop> <PDBx:space_group_symop id="2"> <PDBx:operation_xyz>-x,-y,-z</PDBx:operation_xyz> </PDBx:space_group_symop> <PDBx:space_group_symop id="3"> <PDBx:operation_xyz>-x,1/2+y,1/2-z</PDBx:operation_xyz> </PDBx:space_group_symop> <PDBx:space_group_symop id="4"> <PDBx:operation_xyz>x,1/2-y,1/2+z</PDBx:operation_xyz> </PDBx:space_group_symop> </PDBx:space_group_symopCategory> A parsable string giving one of the symmetry operations of the space group in algebraic form. If W is a matrix representation of the rotational part of the symmetry operation defined by the positions and signs of x, y and z, and w is a column of translations defined by the fractions, an equivalent position X' is generated from a given position X by the equation X' = WX + w (Note: X is used to represent bold_italics_x in International Tables for Crystallography Vol. A, Part 5) When a list of symmetry operations is given, it must contain a complete set of coordinate representatives which generates all the operations of the space group by the addition of all primitive translations of the space group. Such representatives are to be found as the coordinates of the general-equivalent position in International Tables for Crystallography Vol. A (2002), to which it is necessary to add any centring translations shown above the general-equivalent position. That is to say, it is necessary to list explicity all the symmetry operations required to generate all the atoms in the unit cell defined by the setting used. glide reflection through the plane (x,1/4,z), with glide vector 1/2 c x,1/2-y,1/2+z This must match a particular value of attribute id in category space_group, allowing the symmetry operation to be identified with a particular space group. An arbitrary identifier that uniquely labels each symmetry operation in the list. Data items in the STRUCT category record details about the description of the crystallographic structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:structCategory> <PDBx:struct entry_id="5HVP"> <PDBx:title> HIV-1 protease complex with acetyl-pepstatin</PDBx:title> </PDBx:struct> </PDBx:structCategory> The item indicates whether the entry is a CASP target, a CASD-NMR target, or similar target participating in methods development experiments. Y This data item is the X component of a calculation of the center of mass of polymer chains This data item is the Y component of a calculation of the center of mass of polymer chains This data item is the Z component of a calculation of the center of mass of polymer chains An automatically generated descriptor for an NDB structure or the unstructured content of the PDB COMPND record. 5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3' Additional remarks related to this structure deposition that have not been included in details data items elsewhere. Hydrogen bonds between peptide chains follow the Rich and Crick model II for collagen. Estimated formula mass in daltons of the deposited structure assembly. Method used to determine attribute pdbx_formula_weight in category struct. MASS SPEC CALCULATION Text description of the methodology which produced this model structure. This model was produced from a 10 nanosecond Amber/MD simulation starting from PDB structure ID 1ABC. A description of the type of structure model. MINIMIZED AVERAGE A title for the experiment or analysis that is represented in the entry. The default value is the primary citation of the entry. Structure of a B-DNA Dodecamer. Conformation and Dynamic. A title for the data block. The author should attempt to convey the essence of the structure archived in the CIF in the title, and to distinguish this structural result from others. 5'-D(*(I)CP*CP*GP*G)-3 T4 lysozyme mutant - S32A hen egg white lysozyme at -30 degrees C quail egg white lysozyme at 2 atmospheres This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_asymCategory> <PDBx:struct_asym id="A"> <PDBx:details>one monomer of the dimeric enzyme</PDBx:details> <PDBx:entity_id>1</PDBx:entity_id> </PDBx:struct_asym> <PDBx:struct_asym id="B"> <PDBx:details>one monomer of the dimeric enzyme</PDBx:details> <PDBx:entity_id>1</PDBx:entity_id> </PDBx:struct_asym> <PDBx:struct_asym id="C"> <PDBx:details>one partially occupied position for the inhibitor</PDBx:details> <PDBx:entity_id>2</PDBx:entity_id> </PDBx:struct_asym> <PDBx:struct_asym id="D"> <PDBx:details>one partially occupied position for the inhibitor</PDBx:details> <PDBx:entity_id>2</PDBx:entity_id> </PDBx:struct_asym> </PDBx:struct_asymCategory> A description of special aspects of this portion of the contents of the asymmetric unit. The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. This data item is a pointer to attribute id in category entity in the ENTITY category. This data item is a pointer to attribute pdbx_PDB_strand_id in category atom_site the ATOM_SITE category. 1ABC This data item is a pointer to attribute ndb_alias_strand_id in category atom_site the ATOM_SITE category. A flag indicating that this entity was originally labeled with a blank PDB chain id. This data item indicates wheather the structural elements exists only as part of its whole molecule in the asymmetric unit. half This data item provides the information of how many residues which do appear in the SEQRES record are missing at the beginning of the strand. This data item provides the information of how many residues which do not appear in the SEQRES record are missing at the beginning of the strand. This data item provides the information of how many residues which do not appear in the SEQRES record are missing at the end of the strand. This data item indicates whether the structural elements are modified. y This data item gives the order of the structural elements in the ATOM_SITE category. This data item describes the general type of the structural elements in the ATOM_SITE category. The value of attribute id in category struct_asym must uniquely identify a record in the STRUCT_ASYM list. Note that this item need not be a number; it can be any unique identifier. 1 A 2B3 Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light- and heavy-chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_biolCategory> <PDBx:struct_biol id="1"> <PDBx:details> significant deviations from twofold symmetry exist in this dimeric enzyme</PDBx:details> </PDBx:struct_biol> <PDBx:struct_biol id="2"> <PDBx:details> The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (2) is roughly twofold symmetric to biological unit (3). Disorder in the protein chain indicated with alternative ID 1 should be used with this biological unit.</PDBx:details> </PDBx:struct_biol> <PDBx:struct_biol id="3"> <PDBx:details> The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit.</PDBx:details> </PDBx:struct_biol> </PDBx:struct_biolCategory> A description of special aspects of the biological unit. The drug binds to this enzyme in two roughly twofold symmetric modes. Hence this biological unit (3) is roughly twofold symmetric to biological unit (2). Disorder in the protein chain indicated with alternative ID 2 should be used with this biological unit. A description of the structural aggregation in this assembly. The method or experiment used to determine this assembly. AUTHOR PROVIDED', 'LCMS', 'PISA', 'PQS Estimated formula mass in daltons of the biological assembly. Method used to determine attribute pdbx_formula_weight in category struct_biol. MASS SPEC CALCULATION An identifier for the parent biological assembly if this biological unit is part of a complex assembly. 1 2 3 The value of attribute id in category struct_biol must uniquely identify a record in the STRUCT_BIOL list. Note that this item need not be a number; it can be any unique identifier. Data items in the STRUCT_BIOL_GEN category record details about the generation of each biological unit. The STRUCT_BIOL_GEN data items provide the specifications of the components that constitute that biological unit, which may include symmetry elements. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_biol_genCategory> <PDBx:struct_biol_gen asym_id="A" biol_id="1" symmetry="1_555"></PDBx:struct_biol_gen> <PDBx:struct_biol_gen asym_id="B" biol_id="1" symmetry="1_555"></PDBx:struct_biol_gen> <PDBx:struct_biol_gen asym_id="A" biol_id="2" symmetry="1_555"></PDBx:struct_biol_gen> <PDBx:struct_biol_gen asym_id="B" biol_id="2" symmetry="1_555"></PDBx:struct_biol_gen> <PDBx:struct_biol_gen asym_id="C" biol_id="2" symmetry="1_555"></PDBx:struct_biol_gen> <PDBx:struct_biol_gen asym_id="A" biol_id="3" symmetry="1_555"></PDBx:struct_biol_gen> <PDBx:struct_biol_gen asym_id="B" biol_id="3" symmetry="1_555"></PDBx:struct_biol_gen> <PDBx:struct_biol_gen asym_id="D" biol_id="3" symmetry="1_555"></PDBx:struct_biol_gen> </PDBx:struct_biol_genCategory> A description of special aspects of the symmetry generation of this portion of the biological structure. The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. An ordering index used to reproduce the presentation of chain order in the original PDB format data files. 1 2 3 The new residue number after generation of portions of the biomolecule. The new residue number after generation of portions of the biomolecule. The number of the first residue to which the symmetry operations have to be applied to generate a portion of the biomolecule. The number of the last residue to which the symmetry operations have to be applied to generate a portion of the biomolecule. Gives rgb color code of this strand. 0.6 Gives rgb color code of this strand. 0.6 Gives rgb color code of this strand. 0.6 This item expresses category attribute symmetry in category struct_biol_gen on an X, Y and Z basis. -X, Y+1/2, -Z This category gives the NDB strand ids for the complete biomolecule after it is generated. A B This data item is the PDB strand ID of the strand which will be generated. A B This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL category. Describes the symmetry operation that should be applied to the atom set specified by attribute asym_id in category struct_biol_gen to generate a portion of the biological structure. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 Data items in the STRUCT_BIOL_KEYWORDS category record keywords that describe each biological unit. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_biol_keywordsCategory> <PDBx:struct_biol_keywords biol_id="1" text="aspartyl-protease"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="aspartic-protease"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="acid-protease"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="aspartyl-proteinase"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="aspartic-proteinase"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="acid-proteinase"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="enzyme"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="protease"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="proteinase"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="1" text="dimer"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="2" text="drug-enzyme complex"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="2" text="inhibitor-enzyme complex"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="2" text="drug-protease complex"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="2" text="inhibitor-protease complex"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="3" text="drug-enzyme complex"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="3" text="inhibitor-enzyme complex"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="3" text="drug-protease complex"></PDBx:struct_biol_keywords> <PDBx:struct_biol_keywords biol_id="3" text="inhibitor-protease complex"></PDBx:struct_biol_keywords> </PDBx:struct_biol_keywordsCategory> This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL category. Keywords describing this biological entity. antibody antigen enzyme cytokine tRNA Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure. Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry, (1989), 28, 310-320]. <PDBx:struct_biol_viewCategory> <PDBx:struct_biol_view biol_id="c1" id="1"> <PDBx:details> This view highlights the ATAT-Netropsin interaction in the DNA-drug complex.</PDBx:details> <PDBx:rot_matrix11>0.132</PDBx:rot_matrix11> <PDBx:rot_matrix12>0.922</PDBx:rot_matrix12> <PDBx:rot_matrix13>-0.363</PDBx:rot_matrix13> <PDBx:rot_matrix21>0.131</PDBx:rot_matrix21> <PDBx:rot_matrix22>-0.380</PDBx:rot_matrix22> <PDBx:rot_matrix23>-0.916</PDBx:rot_matrix23> <PDBx:rot_matrix31>-0.982</PDBx:rot_matrix31> <PDBx:rot_matrix32>0.073</PDBx:rot_matrix32> <PDBx:rot_matrix33>-0.172</PDBx:rot_matrix33> </PDBx:struct_biol_view> </PDBx:struct_biol_viewCategory> A description of special aspects of this view of the biological structure. This data item can be used as a figure legend. The enzyme has been oriented with the molecular twofold axis aligned with the horizontal axis of the figure. translation vector[1] translation vector[2] translation vector[3] The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_BIOL_GEN category to give a view useful for describing the structure. The conventions used in the rotation are described in attribute details. in category struct_biol_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL category. The value of attribute id in category struct_biol_view must uniquely identify a record in the STRUCT_BIOL_VIEW list. Note that this item need not be a number; it can be any unique identifier. Figure 1 unliganded enzyme view down enzyme active site Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. Data items in the STRUCT_CONF_TYPE category define the criteria used to identify the backbone conformations. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_confCategory> <PDBx:struct_conf id="HELX1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ARG</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>87</PDBx:beg_label_seq_id> <PDBx:conf_type_id>HELX_RH_AL_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLN</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>92</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="HELX2"> <PDBx:beg_label_asym_id>B</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ARG</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>287</PDBx:beg_label_seq_id> <PDBx:conf_type_id>HELX_RH_AL_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>B</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLN</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>292</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="STRN1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>1</PDBx:beg_label_seq_id> <PDBx:conf_type_id>STRN_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>LEU</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>5</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="STRN2"> <PDBx:beg_label_asym_id>B</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>CYS</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>295</PDBx:beg_label_seq_id> <PDBx:conf_type_id>STRN_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>B</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>PHE</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>299</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="STRN3"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>CYS</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>95</PDBx:beg_label_seq_id> <PDBx:conf_type_id>STRN_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>PHE</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>299</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="STRN4"> <PDBx:beg_label_asym_id>B</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>201</PDBx:beg_label_seq_id> <PDBx:conf_type_id>STRN_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>B</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>LEU</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>205</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="TURN1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ILE</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>15</PDBx:beg_label_seq_id> <PDBx:conf_type_id>TURN_TY1P_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLN</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>18</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="TURN2"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>GLY</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>49</PDBx:beg_label_seq_id> <PDBx:conf_type_id>TURN_TY2_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>52</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="TURN3"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ILE</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>55</PDBx:beg_label_seq_id> <PDBx:conf_type_id>TURN_TY1P_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>HIS</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>69</PDBx:end_label_seq_id> </PDBx:struct_conf> <PDBx:struct_conf id="TURN4"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>THR</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>91</PDBx:beg_label_seq_id> <PDBx:conf_type_id>TURN_TY1_P</PDBx:conf_type_id> <PDBx:details xsi:nil="true" /> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>94</PDBx:end_label_seq_id> </PDBx:struct_conf> </PDBx:struct_confCategory> A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute id in category struct_conf_type in the STRUCT_CONF_TYPE category. A description of special aspects of the conformation assignment. A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the conformation segment ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This item is a place holder for the helix class used in the PDB HELIX record. A placeholder for the helix identifier of the PDB HELIX record. A placeholder for the lengths of the helix of the PDB HELIX record. A component of the identifier for the residue at which the conformation segment starts. A component of the identifier for the residue at which the conformation segment ends. The value of attribute id in category struct_conf must uniquely identify a record in the STRUCT_CONF list. Note that this item need not be a number; it can be any unique identifier. Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_conf_typeCategory> <PDBx:struct_conf_type id="HELX_RH_AL_P"> <PDBx:criteria>author judgement</PDBx:criteria> <PDBx:reference xsi:nil="true" /> </PDBx:struct_conf_type> <PDBx:struct_conf_type id="STRN_P"> <PDBx:criteria>author judgement</PDBx:criteria> <PDBx:reference xsi:nil="true" /> </PDBx:struct_conf_type> <PDBx:struct_conf_type id="TURN_TY1_P"> <PDBx:criteria>author judgement</PDBx:criteria> <PDBx:reference xsi:nil="true" /> </PDBx:struct_conf_type> <PDBx:struct_conf_type id="TURN_TY1P_P"> <PDBx:criteria>author judgement</PDBx:criteria> <PDBx:reference xsi:nil="true" /> </PDBx:struct_conf_type> <PDBx:struct_conf_type id="TURN_TY2_P"> <PDBx:criteria>author judgement</PDBx:criteria> <PDBx:reference xsi:nil="true" /> </PDBx:struct_conf_type> <PDBx:struct_conf_type id="TURN_TY2P_P"> <PDBx:criteria>author judgement</PDBx:criteria> <PDBx:reference xsi:nil="true" /> </PDBx:struct_conf_type> </PDBx:struct_conf_typeCategory> The criteria used to assign this conformation type. author judgement phi=54-74, psi=30-50 A literature reference that defines the criteria used to assign this conformation type and subtype. The descriptor that categorizes the type of the conformation of the backbone of the polymer (whether protein or nucleic acid). Explicit values for the torsion angles that define each conformation are not given here, but it is expected that the author would provide such information in either the _struct_conf_type.criteria or _struct_conf_type.reference data items, or both. Data items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on. The STRUCT_CONN_TYPE records define the criteria used to identify these connections. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_connCategory> <PDBx:struct_conn id="C1"> <PDBx:conn_type_id>saltbr</PDBx:conn_type_id> <PDBx:details xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>A</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>NZ1</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ARG</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>87</PDBx:ptnr1_label_seq_id> <PDBx:ptnr1_role>positive</PDBx:ptnr1_role> <PDBx:ptnr1_symmetry>1_555</PDBx:ptnr1_symmetry> <PDBx:ptnr2_label_asym_id>A</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id>OE1</PDBx:ptnr2_label_atom_id> <PDBx:ptnr2_label_comp_id>GLU</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>92</PDBx:ptnr2_label_seq_id> <PDBx:ptnr2_role>negative</PDBx:ptnr2_role> <PDBx:ptnr2_symmetry>1_555</PDBx:ptnr2_symmetry> </PDBx:struct_conn> <PDBx:struct_conn id="C2"> <PDBx:conn_type_id>hydrog</PDBx:conn_type_id> <PDBx:details xsi:nil="true" /> <PDBx:ptnr1_label_asym_id>B</PDBx:ptnr1_label_asym_id> <PDBx:ptnr1_label_atom_id>N</PDBx:ptnr1_label_atom_id> <PDBx:ptnr1_label_comp_id>ARG</PDBx:ptnr1_label_comp_id> <PDBx:ptnr1_label_seq_id>287</PDBx:ptnr1_label_seq_id> <PDBx:ptnr1_role>donor</PDBx:ptnr1_role> <PDBx:ptnr1_symmetry>1_555</PDBx:ptnr1_symmetry> <PDBx:ptnr2_label_asym_id>B</PDBx:ptnr2_label_asym_id> <PDBx:ptnr2_label_atom_id>O</PDBx:ptnr2_label_atom_id> <PDBx:ptnr2_label_comp_id>GLY</PDBx:ptnr2_label_comp_id> <PDBx:ptnr2_label_seq_id>292</PDBx:ptnr2_label_seq_id> <PDBx:ptnr2_role>acceptor</PDBx:ptnr2_role> <PDBx:ptnr2_symmetry>1_555</PDBx:ptnr2_symmetry> </PDBx:struct_conn> </PDBx:struct_connCategory> This data item is a pointer to attribute id in category struct_conn_type in the STRUCT_CONN_TYPE category. A description of special aspects of the connection. disulfide bridge C-S-S-C is highly distorted A placeholder for the PDB id in the case the category is used to hold the information of the MODRES record of a PDB file. 1ABC Distance value for this contact. This data item identifies if the linkage has displaced leaving atoms on both, one or none of the connected atoms forming the linkage. Leaving atoms are defined within their chemical defintions of each connected component. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. 1 2 The chiral configuration of the first atom making the linkage. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A B A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A B The leaving atom that is removed from first atom making the linkage. The abbreviation of the modifier group. bromine atom BR cis-platinum-(NH3)2 PT(NH3)2 The name of the atom which got replaced by the modifier. O4* A placeholder for the standard residue name found in the MODRES record of a PDB file. A T C G GLY ALA MET The abbreviation of the sugar modifier in the case it is a conformer of deoxyribose or ribose. arabinose ARA A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. 1 2 The chiral configuration of the second atom making the linkage. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A B A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A B The leaving atom that is removed from second atom making the linkage. A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. 1 2 A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute pdbx_auth_alt_id in category atom_site in the ATOM_SITE category. A B A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A B C A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. O5* A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A T C G GLY ALA MET A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute pdbx_PDB_ins_code in category atom_site in the ATOM_SITE category. 1 2 A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. 12 A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute label_alt_id in category atom_site in the ATOM_SITE category. A B A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A B C A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. O5* A component of the identifier for partner 3 of the structure connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A T C G GLY ALA MET A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. 12 The chemical or structural role of the interaction N-Glycosylation O-Glycosylation The chemical bond order associated with the specified atoms in this contact. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 1 of the structure connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The chemical or structural role of the first partner in the structure connection. donor acceptor negative positive metal metal coordination Describes the symmetry operation that should be applied to the atom set specified by attribute ptnr1_label* in category struct_conn to generate the first partner in the structure connection. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for partner 2 of the structure connection. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. The chemical or structural role of the second partner in the structure connection. donor acceptor negative positive metal metal coordination Describes the symmetry operation that should be applied to the atom set specified by attribute ptnr2_label* in category struct_conn to generate the second partner in the structure connection. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The value of attribute id in category struct_conn must uniquely identify a record in the STRUCT_CONN list. Note that this item need not be a number; it can be any unique identifier. Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_conn_typeCategory> <PDBx:struct_conn_type id="saltbr"> <PDBx:criteria>negative to positive distance &gt; 2.5 \&#37;A, &lt; 3.2 \&#37;A</PDBx:criteria> <PDBx:reference xsi:nil="true" /> </PDBx:struct_conn_type> <PDBx:struct_conn_type id="hydrog"> <PDBx:criteria>NO distance &gt; 2.5\&#37;A, &lt; 3.5\&#37;A, NOC angle &lt; 120 degrees</PDBx:criteria> <PDBx:reference xsi:nil="true" /> </PDBx:struct_conn_type> </PDBx:struct_conn_typeCategory> The criteria used to define the interaction. O to N distance > 2.5 \%A, < 3.2 \%A authors judgement A reference that specifies the criteria used to define the interaction. The chemical or structural type of the interaction. Data items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_keywordsCategory> <PDBx:struct_keywords entry_id="5HVP"> <PDBx:text>enzyme-inhibitor complex, aspartyl protease, static disorder</PDBx:text> </PDBx:struct_keywords> </PDBx:struct_keywordsCategory> Keywords describing this structure. This is constructed by the PROGRAM for the PDB KEYWRD record. B-DNA, DOUBLE HELIX, MODIFIED B-DNA, DOUBLE HELIX, FLIPPED OUT BASES Terms characterizing the macromolecular structure. DNA RNA T-RNA DNA/RNA RIBOZYME PROTEIN/DNA PROTEIN/RNA PEPTIDE NUCLEIC ACID PEPTIDE NUCLEIC ACID/DNA DNA-BINDING PROTEIN RNA-BINDING PROTEIN Keywords describing this structure. serine protease inhibited complex high-resolution refinement This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the STRUCT_MON_DETAILS category record details about specifics of calculations summarized in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can include the coefficients used in map calculations, the radii used for including points in a calculation and so on. This data item describes the specifics of the calculations that generated the values given in attribute RSCC_all, in category struct_mon_prot _struct_mon_prot.RSCC_main and _struct_mon_prot.RSCC_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation. The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Map grid points within 1.5 A of the designated atoms were included in the calculation. The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure-factor amplitudes and phases, respectively, calculated from the current model. Map grid points within a van der Waals radius of the designated atoms were included in the calculation. This data item describes the specifics of the calculations that generated the values given in attribute RSR_all, in category struct_mon_prot _struct_mon_prot.RSR_main and _struct_mon_prot.RSR_side. The coefficients used to calculate the p(o) and p(c) maps should be given as well as the criterion for the inclusion of map grid points in the calculation. The map p(o) was calculated with coefficients 2F(o) - F(c) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, F(c) are the amplitudes calculated from the current model and alpha(c) are the phases calculated from the current model. The map p(c) was calculated in program O using a Gaussian distribution function around the atoms in the current model. Map grid points within 1.5 A of the designated atoms were included in the calculation. The map p(o) was calculated with coefficients F(o) and with phase alpha(c). F(o) are the observed structure-factor amplitudes, and alpha(c) are the phases calculated from the current model. The map p(c) was calculated with coefficients F(c) and with phases alpha(c). F(c) and alpha(c) are the structure-factor amplitudes and phases, respectively, calculated from the current model. Map grid points within a van der Waals radius of the designated atoms were included in the calculation. An ideal cis peptide bond would have an omega torsion angle of zero. This data item gives the value in degrees by which the observed torsion angle can differ from 0.0 and still be considered cis. 30.0 This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the STRUCT_MON_NUCL category record details about structural properties of a nucleic acid when analyzed at the monomer level. Analogous data items for proteins are given in the STRUCT_MON_PROT category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category. Example 1 - based on NDB structure BDL028. <PDBx:struct_mon_nuclCategory> <PDBx:struct_mon_nucl label_alt_id="A" label_asym_id="A" label_comp_id="C" label_seq_id="1"> <PDBx:alpha xsi:nil="true" /> <PDBx:beta xsi:nil="true" /> <PDBx:delta>131.9</PDBx:delta> <PDBx:epsilon>222.1</PDBx:epsilon> <PDBx:gamma>29.9</PDBx:gamma> <PDBx:zeta>174.2</PDBx:zeta> </PDBx:struct_mon_nucl> <PDBx:struct_mon_nucl label_alt_id="A" label_asym_id="A" label_comp_id="G" label_seq_id="2"> <PDBx:alpha>334.0</PDBx:alpha> <PDBx:beta>130.6</PDBx:beta> <PDBx:delta>125.6</PDBx:delta> <PDBx:epsilon>167.6</PDBx:epsilon> <PDBx:gamma>33.1</PDBx:gamma> <PDBx:zeta>270.9</PDBx:zeta> </PDBx:struct_mon_nucl> <PDBx:struct_mon_nucl label_alt_id="A" label_asym_id="A" label_comp_id="T" label_seq_id="3"> <PDBx:alpha>258.2</PDBx:alpha> <PDBx:beta>178.7</PDBx:beta> <PDBx:delta>114.6</PDBx:delta> <PDBx:epsilon>216.6</PDBx:epsilon> <PDBx:gamma>101.0</PDBx:gamma> <PDBx:zeta>259.3</PDBx:zeta> </PDBx:struct_mon_nucl> </PDBx:struct_mon_nuclCategory> P is the phase angle of pseudorotation for five-membered rings. For ribose and deoxyribose sugars in nucleic acids (tau4 +tau1)-(tau3+tau0) P = ATAN (-------------------------) 2tau2 (sin 36+sin 72) If tau2 is <0, then P=P+180 degree (Altona & Sundaralingam, 1972). Ref: Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205-8212. The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the nucleic acid monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the base moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the phosphate moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the sugar moiety of the nucleic acid monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. The value in degrees of the backbone torsion angle alpha (O3'-P-O5'-C5'). A component of the identifier for participants in the site. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value in degrees of the backbone torsion angle beta (P-O5'-C5'-C4'). The value in degrees of the sugar-base torsion angle chi1 (O4'-C1'-N1-C2). The value in degrees of the sugar-base torsion angle chi2 (O4'-C1'-N9-C4). The value in degrees of the backbone torsion angle delta (C5'-C4'-C3'-O3'). A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation. Part of the phosphodiester backbone not in density. The value in degrees of the backbone torsion angle epsilon (C4'-C3'-O3'-P). The value in degrees of the backbone torsion angle gamma (O5'-C5'-C4'-C3'). The mean value of the isotropic displacement parameter for all atoms in the monomer. The mean value of the isotropic displacement parameter for atoms in the base moiety of the nucleic acid monomer. The mean value of the isotropic displacement parameter for atoms in the phosphate moiety of the nucleic acid monomer. The mean value of the isotropic displacement parameter for atoms in the sugar moiety of the nucleic acid monomer. The value in degrees of the sugar torsion angle nu0 (C4'-O4'-C1'-C2'). The value in degrees of the sugar torsion angle nu1 (O4'-C1'-C2'-C3'). The value in degrees of the sugar torsion angle nu2 (C1'-C2'-C3'-C4'). The value in degrees of the sugar torsion angle nu3 (C2'-C3'-C4'-O4'). The value in degrees of the sugar torsion angle nu4 (C3'-C4'-O4'-C1'). The value in degrees of the sugar torsion angle tau0 (C4'-O4'-C1'-C2'). The value in degrees of the sugar torsion angle tau1 (O4'-C1'-C2'-C3'). The value in degrees of the sugar torsion angle tau2 (C1'-C2'-C3'-C4'). The value in degrees of the sugar torsion angle tau3 (C2'-C3'-C4'-O4'). The value in degrees of the sugar torsion angle tau4 (C3'-C4'-O4'-C1'). The maximum amplitude of puckering. This is derived from the pseudorotation value P and the torsion angles in the ribose ring. Tau2= Taum cosP Tau3= Taum cos(P+144) Tau4= Taum cos(P+288) Tau0= Taum cos(P+ 72) Tau1= Taum cos(P+216) The value in degrees of the backbone torsion angle zeta (C3'-O3'-P-O5'). A component of the identifier for participants in the site. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for participants in the site. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category. Example 1 - based on laboratory records for protein NS1. This example provides details for residue ARG 35. <PDBx:struct_mon_protCategory> <PDBx:struct_mon_prot label_alt_id="A" label_asym_id="A" label_comp_id="ARG" label_seq_id="35"> <PDBx:RSCC_all>0.90</PDBx:RSCC_all> <PDBx:RSR_all>0.18</PDBx:RSR_all> <PDBx:chi1>-67.9</PDBx:chi1> <PDBx:chi2>-174.7</PDBx:chi2> <PDBx:chi3>-67.7</PDBx:chi3> <PDBx:chi4>-86.3</PDBx:chi4> <PDBx:chi5>4.2</PDBx:chi5> <PDBx:mean_B_all>30.0</PDBx:mean_B_all> <PDBx:mean_B_main>25.0</PDBx:mean_B_main> <PDBx:mean_B_side>35.1</PDBx:mean_B_side> <PDBx:omega>180.1</PDBx:omega> <PDBx:phi>-60.3</PDBx:phi> <PDBx:psi>-46.0</PDBx:psi> </PDBx:struct_mon_prot> </PDBx:struct_mon_protCategory> The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the main chain of the monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. The real-space (linear) correlation coefficient RSCC, as described by Jones et al. (1991), evaluated over all atoms in the side chain of the monomer. sum|p~obs~ - <p~obs~>| * sum|p~calc~ - <p~calc~>| RSCC = ------------------------------------------------- [ sum|p~obs~ - <p~obs~> |^2^ * sum|p~calc~ - <p~calc~>|^2^ ]^1/2^ p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSCC in category struct_mon_details. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSCC. in category struct_mon_details Ref: Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119. The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the main chain of the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. The real-space residual RSR, as described by Branden & Jones (1990), evaluated over all atoms in the side chain of the monomer. sum|p~obs~ - p~calc~| RSR = --------------------- sum|p~obs~ + p~calc~| p~obs~ = the density in an 'experimental' map p~calc~ = the density in a 'calculated' map sum is taken over the specified grid points Details of how these maps were calculated should be given in attribute RSR in category struct_mon_details. The sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in attribute RSR. in category struct_mon_details Ref: Branden, C.-I. & Jones, T. A. (1990). Nature (London), 343, 687-689. A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. The value in degrees of the side-chain torsion angle chi1, for those residues containing such an angle. The value in degrees of the side-chain torsion angle chi2, for those residues containing such an angle. The value in degrees of the side-chain torsion angle chi3, for those residues containing such an angle. The value in degrees of the side-chain torsion angle chi4, for those residues containing such an angle. The value in degrees of the side-chain torsion angle chi5, for those residues containing such an angle. A description of special aspects of the residue, its conformation, behaviour in refinement, or any other aspect that requires annotation. very poor density The side chain of this density may occupy alternative conformations, but alternative conformations were not fit in this model. This residue has a close contact with the bound inhibitor, which may account for the nonstandard conformation of the side chain. The mean value of the isotropic displacement parameter for all atoms in the monomer. The mean value of the isotropic displacement parameter for atoms in the main chain of the monomer. The mean value of the isotropic displacement parameter for atoms in the side chain of the monomer. The value in degrees of the main-chain torsion angle omega. The value in degrees of the main-chain torsion angle phi. The value in degrees of the main-chain torsion angle psi. A component of the identifier for the monomer. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for the monomer. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Data items in the STRUCT_MON_PROT_CIS category identify monomers that have been found to have the peptide bond in the cis conformation. The criterion used to select residues to be designated as containing cis peptide bonds is given in attribute prot_cis in category struct_mon_details. Example 1 - based on PDB structure 1ACY of Ghiara, Stura, Stanfield, Profy & Wilson [Science (1994), 264, 82-85]. <PDBx:struct_mon_prot_cisCategory> <PDBx:struct_mon_prot_cis pdbx_id="1"> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>L</PDBx:label_asym_id> <PDBx:label_comp_id>PRO</PDBx:label_comp_id> <PDBx:label_seq_id>8</PDBx:label_seq_id> <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num> </PDBx:struct_mon_prot_cis> <PDBx:struct_mon_prot_cis pdbx_id="2"> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>L</PDBx:label_asym_id> <PDBx:label_comp_id>PRO</PDBx:label_comp_id> <PDBx:label_seq_id>77</PDBx:label_seq_id> <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num> </PDBx:struct_mon_prot_cis> <PDBx:struct_mon_prot_cis pdbx_id="3"> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>L</PDBx:label_asym_id> <PDBx:label_comp_id>PRO</PDBx:label_comp_id> <PDBx:label_seq_id>95</PDBx:label_seq_id> <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num> </PDBx:struct_mon_prot_cis> <PDBx:struct_mon_prot_cis pdbx_id="4"> <PDBx:label_alt_id xsi:nil="true" /> <PDBx:label_asym_id>L</PDBx:label_asym_id> <PDBx:label_comp_id>PRO</PDBx:label_comp_id> <PDBx:label_seq_id>141</PDBx:label_seq_id> <PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num> </PDBx:struct_mon_prot_cis> </PDBx:struct_mon_prot_cisCategory> A component of the identifier for the monomer. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for the monomer. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. Pointer to attribute pdbx_PDB_ins_code in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site Pointer to attribute pdbx_PDB_model_num in category atom_site Pointer to attribute auth_asym_id in category atom_site. Pointer to attribute auth_comp_id in category atom_site. PDB Insertion code PDB Insertion code Pointer to attribute auth_seq_id in category atom_site Pointer to attribute label_asym_id in category atom_site. Pointer to attribute label_comp_id in category atom_site. Pointer to attribute label_seq_id in category atom_site omega torsion angle ordinal index Data items in the STRUCT_NCS_DOM category record information about the domains in an ensemble of domains related by one or more noncrystallographic symmetry operators. A domain need not correspond to a complete polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <PDBx:struct_ncs_domCategory> <PDBx:struct_ncs_dom id="d1" pdbx_ens_id="1"> <PDBx:details>Chains A, B, and C</PDBx:details> </PDBx:struct_ncs_dom> <PDBx:struct_ncs_dom id="d2" pdbx_ens_id="1"> <PDBx:details>Chains D, E, and F</PDBx:details> </PDBx:struct_ncs_dom> </PDBx:struct_ncs_domCategory> A description of special aspects of the structural elements that comprise a domain in an ensemble of domains related by noncrystallographic symmetry. The loop between residues 18 and 23 in this domain interacts with a symmetry-related molecule, and thus deviates significantly from the noncrystallographic threefold. The value of attribute id in category struct_ncs_dom must uniquely identify a record in the STRUCT_NCS_DOM list. Note that this item need not be a number; it can be any unique identifier. This is a unique identifier for a collection NCS related domains. This references item '_struct_ncs_ens.id'. Data items in the STRUCT_NCS_DOM_LIM category identify the start and end points of polypeptide chain segments that form all or part of a domain in an ensemble of domains related by noncrystallographic symmetry. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <PDBx:struct_ncs_dom_limCategory> <PDBx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="1" pdbx_ens_id="1"> <PDBx:beg_label_alt_id xsi:nil="true" /> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>1</PDBx:beg_label_seq_id> <PDBx:end_label_alt_id xsi:nil="true" /> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>29</PDBx:end_label_seq_id> </PDBx:struct_ncs_dom_lim> <PDBx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="2" pdbx_ens_id="1"> <PDBx:beg_label_alt_id xsi:nil="true" /> <PDBx:beg_label_asym_id>B</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>31</PDBx:beg_label_seq_id> <PDBx:end_label_alt_id xsi:nil="true" /> <PDBx:end_label_asym_id>B</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>59</PDBx:end_label_seq_id> </PDBx:struct_ncs_dom_lim> <PDBx:struct_ncs_dom_lim dom_id="d1" pdbx_component_id="3" pdbx_ens_id="1"> <PDBx:beg_label_alt_id xsi:nil="true" /> <PDBx:beg_label_asym_id>C</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>61</PDBx:beg_label_seq_id> <PDBx:end_label_alt_id xsi:nil="true" /> <PDBx:end_label_asym_id>B</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>89</PDBx:end_label_seq_id> </PDBx:struct_ncs_dom_lim> <PDBx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="1" pdbx_ens_id="1"> <PDBx:beg_label_alt_id xsi:nil="true" /> <PDBx:beg_label_asym_id>D</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>91</PDBx:beg_label_seq_id> <PDBx:end_label_alt_id xsi:nil="true" /> <PDBx:end_label_asym_id>D</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>119</PDBx:end_label_seq_id> </PDBx:struct_ncs_dom_lim> <PDBx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="2" pdbx_ens_id="1"> <PDBx:beg_label_alt_id xsi:nil="true" /> <PDBx:beg_label_asym_id>E</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>121</PDBx:beg_label_seq_id> <PDBx:end_label_alt_id xsi:nil="true" /> <PDBx:end_label_asym_id>E</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>149</PDBx:end_label_seq_id> </PDBx:struct_ncs_dom_lim> <PDBx:struct_ncs_dom_lim dom_id="d2" pdbx_component_id="3" pdbx_ens_id="1"> <PDBx:beg_label_alt_id xsi:nil="true" /> <PDBx:beg_label_asym_id>F</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>PRO</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>151</PDBx:beg_label_seq_id> <PDBx:end_label_alt_id xsi:nil="true" /> <PDBx:end_label_asym_id>F</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>GLY</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>179</PDBx:end_label_seq_id> </PDBx:struct_ncs_dom_lim> </PDBx:struct_ncs_dom_limCategory> A component of the identifier for the monomer at which this segment of the domain begins. A component of the identifier for the monomer at which this segment of the domain begins. A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the monomer at which this segment of the domain begins. A component of the identifier for the monomer at which this segment of the domain begins. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. A component of the identifier for the monomer at which this segment of the domain begins. A component of the identifier for the monomer at which this segment of the domain begins. A component of the identifier for the monomer at which this segment of the domain ends. A component of the identifier for the monomer at which this segment of the domain ends. A component of the identifier for the monomer at which this segment of the domain ends. A component of the identifier for the monomer at which this segment of the domain ends. A component of the identifier for the monomer at which this segment of the domain ends. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. A component of the identifier for the monomer at which this segment of the domain ends. A component of the identifier for the monomer at which this segment of the domain ends. record the refinement code number (from CCP4.) A text description of the selection of residues that correspond to this domain. This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. Record number of the NCS domain limit assignment. This is a unique identifier for a collection NCS related domains. This references item '_struct_ncs_dom.pdbx_ens_id'. Data items in the STRUCT_NCS_ENS category record information about ensembles of domains related by noncrystallographic symmetry. The point group of the ensemble when taken as a whole may be specified, as well as any special aspects of the ensemble that require description. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <PDBx:struct_ncs_ensCategory> <PDBx:struct_ncs_ens id="en1"> <PDBx:details> The ensemble represents the pseudo-twofold symmetry between domains d1 and d2.</PDBx:details> </PDBx:struct_ncs_ens> </PDBx:struct_ncs_ensCategory> A description of special aspects of the ensemble. The ensemble has a slight translation between domains 1 and 4, but overall it can accurately be described as point group 222 The point group of the ensemble of structural elements related by one or more noncrystallographic symmetry operations. The relationships need not be precise; this data item is intended to give a rough description of the noncrystallographic symmetry relationships. 3 422 non-proper The value of attribute id in category struct_ncs_ens must uniquely identify a record in the STRUCT_NCS_ENS list. Note that this item need not be a number; it can be any unique identifier. Data items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator. Example 1 - based on laboratory records for the collagen-like peptide, HYP-. <PDBx:struct_ncs_ens_genCategory> <PDBx:struct_ncs_ens_gen dom_id_1="d1" dom_id_2="d2" ens_id="en1" oper_id="1"></PDBx:struct_ncs_ens_gen> </PDBx:struct_ncs_ens_genCategory> The identifier for the domain that will remain unchanged by the transformation operator. This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. The identifier for the domain that will be transformed by application of the transformation operator. This data item is a pointer to attribute id in category struct_ncs_dom in the STRUCT_NCS_DOM category. This data item is a pointer to attribute id in category struct_ncs_ens in the STRUCT_NCS_ENS category. This data item is a pointer to attribute id in category struct_ncs_oper in the STRUCT_NCS_OPER category. Data items in the STRUCT_NCS_OPER category describe the noncrystallographic symmetry operations. Each operator is specified as a matrix and a subsequent translation vector. Operators need not represent proper rotations. Example 1 - based on laboratory records for the protein NS1. <PDBx:struct_ncs_operCategory> <PDBx:struct_ncs_oper id="1"> <PDBx:code>given</PDBx:code> <PDBx:details> Matrix and translation vector for pseudo-twofold operation.</PDBx:details> <PDBx:matrix11>0.247</PDBx:matrix11> <PDBx:matrix12>0.935</PDBx:matrix12> <PDBx:matrix13>0.256</PDBx:matrix13> <PDBx:matrix21>0.929</PDBx:matrix21> <PDBx:matrix22>0.153</PDBx:matrix22> <PDBx:matrix23>0.337</PDBx:matrix23> <PDBx:matrix31>0.276</PDBx:matrix31> <PDBx:matrix32>0.321</PDBx:matrix32> <PDBx:matrix33>-0.906</PDBx:matrix33> <PDBx:vector1>-8.253</PDBx:vector1> <PDBx:vector2>-11.743</PDBx:vector2> <PDBx:vector3>-1.782</PDBx:vector3> </PDBx:struct_ncs_oper> </PDBx:struct_ncs_operCategory> A code to indicate whether this operator describes a relationship between coordinates all of which are given in the data block (in which case the value of code is 'given'), or whether the operator is used to generate new coordinates from those that are given in the data block (in which case the value of code is 'generate'). A description of special aspects of the noncrystallographic symmetry operator. The operation is given as a precise threefold rotation, despite the fact the best rms fit between domain 1 and domain 2 yields a rotation of 119.7 degrees and a translation of 0.13 angstroms. The [1][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [1][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [1][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [2][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [2][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [2][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [3][1] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [3][2] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [3][3] element of the 3x3 matrix component of a noncrystallographic symmetry operation. The [1] element of the three-element vector component of a noncrystallographic symmetry operation. The [2] element of the three-element vector component of a noncrystallographic symmetry operation. The [3] element of the three-element vector component of a noncrystallographic symmetry operation. The value of attribute id in category struct_ncs_oper must uniquely identify a record in the STRUCT_NCS_OPER list. Note that for PDB attribute id in category struct_ncs_oper must be a number. Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item attribute seq_align in category struct_ref is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of attribute seq_dif in category struct_ref is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_refCategory> <PDBx:struct_ref id="1"> <PDBx:biol_id xsi:nil="true" /> <PDBx:db_code>12345</PDBx:db_code> <PDBx:db_name>Genbank</PDBx:db_name> <PDBx:details xsi:nil="true" /> <PDBx:entity_id>1</PDBx:entity_id> <PDBx:seq_align>entire</PDBx:seq_align> <PDBx:seq_dif>yes</PDBx:seq_dif> </PDBx:struct_ref> <PDBx:struct_ref id="2"> <PDBx:biol_id>2</PDBx:biol_id> <PDBx:db_code>1ABC</PDBx:db_code> <PDBx:db_name>PDB</PDBx:db_name> <PDBx:details> The structure of the closely related compound, isobutyryl-pepstatin (pepstatin A) in complex with rhizopuspepsin</PDBx:details> <PDBx:entity_id xsi:nil="true" /> <PDBx:seq_align xsi:nil="true" /> <PDBx:seq_dif xsi:nil="true" /> </PDBx:struct_ref> </PDBx:struct_refCategory> This data item is a pointer to attribute id in category struct_biol in the STRUCT_BIOL category. The code for this entity or biological unit or for a closely related entity or biological unit in the named database. 1ABC ABCDEF The name of the database containing reference information about this entity or biological unit. PDB CSD Genbank A description of special aspects of the relationship between the entity or biological unit described in the data block and that in the referenced database entry. This data item is a pointer to attribute id in category entity in the ENTITY category. Beginning index in the chemical sequence from the reference database. 1 2 Ending index in the chemical sequence from the reference database. 105 245 Accession code assigned by the reference database. P07617 Database code assigned by the reference database for a sequence isoform. An isoform sequence is an alternative protein sequence that can be generated from the same gene by a single or by a combination of biological events such as: alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting. P29994-6 Database chemical sequence expressed as string of one-letter amino acid codes. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other A flag to indicate the scope of the alignment between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. 'entire' indicates that alignment spans the entire length of both sequences (although point differences may occur and can be annotated using the data items in the STRUCT_REF_SEQ_DIF category). 'partial' indicates a partial alignment. The region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. This data item may also take the value '.', indicating that the reference is not to a sequence. A flag to indicate the presence ('yes') or absence ('no') of point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. This data item may also take the value '.', indicating that the reference is not to a sequence. The value of attribute id in category struct_ref must uniquely identify a record in the STRUCT_REF list. Note that this item need not be a number; it can be any unique identifier. Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry. Example 1 - based on the sequence alignment of CHER from M. xantus (36 to 288) and CHER from S. typhimurium (18 to 276). <PDBx:struct_ref_seqCategory> <PDBx:struct_ref_seq align_id="alg1"> <PDBx:db_align_beg>18</PDBx:db_align_beg> <PDBx:db_align_end>276</PDBx:db_align_end> <PDBx:details> The alignment contains 3 gaps larger than 2 residues</PDBx:details> <PDBx:ref_id>seqdb1</PDBx:ref_id> <PDBx:seq_align_beg>36</PDBx:seq_align_beg> <PDBx:seq_align_end>288</PDBx:seq_align_end> </PDBx:struct_ref_seq> </PDBx:struct_ref_seqCategory> The sequence position in the referenced database entry at which the alignment begins. The sequence position in the referenced database entry at which the alignment ends. A description of special aspects of the sequence alignment. The PDB code of the structure. 1BBP Initial position in the PDB sequence segment. 1 2 Ending position in the PDB sequence segment 1 2 Accession code of the reference database. P07617 Initial insertion code of the sequence segment of the reference database. 1 2 Ending insertion code of the sequence segment of the reference database. 1 2 Initial insertion code of the PDB sequence segment. 1 2 Ending insertion code of the sequence segment 1 2 The PDB strand/chain ID . A B This data item is a pointer to attribute id in category struct_ref in the STRUCT_REF category. The sequence position in the entity or biological unit described in the data block at which the alignment begins. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. The sequence position in the entity or biological unit described in the data block at which the alignment ends. This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. The value of attribute align_id in category struct_ref_seq must uniquely identify a record in the STRUCT_REF_SEQ list. Note that this item need not be a number; it can be any unique identifier. Data items in the STRUCT_REF_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the referenced database entry. Example 1 - based on laboratory records for CAP-DNA complex. <PDBx:struct_ref_seq_difCategory> <PDBx:struct_ref_seq_dif pdbx_ordinal="1"> <PDBx:align_id>algn2</PDBx:align_id> <PDBx:db_mon_id>GLU</PDBx:db_mon_id> <PDBx:details> A point mutation was introduced in the CAP at position 181 substituting PHE for GLU.</PDBx:details> <PDBx:mon_id>PHE</PDBx:mon_id> <PDBx:seq_num>181</PDBx:seq_num> </PDBx:struct_ref_seq_dif> </PDBx:struct_ref_seq_difCategory> This data item is a pointer to attribute align_id in category struct_ref_seq in the STRUCT_REF_SEQ category. The monomer type found at this position in the referenced database entry. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. A description of special aspects of the point differences between the sequence of the entity or biological unit described in the data block and that in the referenced database entry. The monomer type found at this position in the sequence of the entity or biological unit described in this data block. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. The PDB sequence residue number. 1 2 The PDB ID code. 1BBP Insertion code in PDB sequence 1 2 PDB strand/chain id. A B Sequence database accession number. P07617 Sequence database name. SWS Sequence database sequence number. 142 This data item is a pointer to attribute num in category entity_poly_seq in the ENTITY_POLY_SEQ category. A synthetic integer primary key for this category. Data items in the STRUCT_SHEET category record details about the beta-sheets. Example 1 - simple beta-barrel. N O N O N O N O N O N O 10--11--12--13--14--15--16--17--18--19--20 strand_a N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 30--31--32--33--34--35--36--37--38--39--40 strand_b N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 50--51--52--53--54--55--56--57--58--59--60 strand_c N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 70--71--72--73--74--75--76--77--78--79--80 strand_d N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 90--91--92--93--94--95--96--97--98--99-100 strand_e N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 110-111-112-113-114-115-116-117-118-119-120 strand_f N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 130-131-132-133-134-135-136-137-138-139-140 strand_g N O N O N O N O N O / \ / \ / \ / \ / \ N O N O N O N O N O N O 150-151-152-153-154-155-156-157-158-159-160 strand_h N O N O N O N O N O / \ / \ / \ / \ / \ <PDBx:struct_sheetCategory> <PDBx:struct_sheet id="sheet_1"> <PDBx:details xsi:nil="true" /> <PDBx:number_strands>8</PDBx:number_strands> <PDBx:type>beta-barrel</PDBx:type> </PDBx:struct_sheet> </PDBx:struct_sheetCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. N O N O N O N O -10--11--12--13--14--15--16--17--18-> strand_a N O N O N O N O N O | | | | | | | | | | O N O N O N O N O N <-119-118-117-116-115-114-113-112-111-110- strand_b O N O N O N O N O N \ / \ / \ / \ / \ O N O N O N O N O N O N <-41--40--39--38--37--36--35--34--33--32--31--30- strand_c O N O N O N O N O N O N | | | | | | | | | | | | N O N O N O N O N O N O strand_d1 -50--51--52-> -90--91--92--93--95--95--96--97-> strand_d2 N O N O N O N O N O | | | | | | | | | | | | O N O N O N O N O N O N <-80--79--78--77--76--75--74--73--72--71--70- strand_e O N O N O N O N O N <PDBx:struct_sheetCategory> <PDBx:struct_sheet id="sheet_2"> <PDBx:details>strand_d is in two pieces</PDBx:details> <PDBx:number_strands>5</PDBx:number_strands> <PDBx:type>five stranded, mixed-sense</PDBx:type> </PDBx:struct_sheet> </PDBx:struct_sheetCategory> A description of special aspects of the beta-sheet. The number of strands in the sheet. If a given range of residues bulges out from the strands, it is still counted as one strand. If a strand is composed of two different regions of polypeptide, it is still counted as one strand, as long as the proper hydrogen- bonding connections are made to adjacent strands. A simple descriptor for the type of the sheet. jelly-roll Rossmann fold beta barrel The value of attribute id in category struct_sheet must uniquely identify a record in the STRUCT_SHEET list. Note that this item need not be a number; it can be any unique identifier. Data items in the STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta- sheet. It is necessary to treat hydrogen bonding independently of the designation of ranges, because the hydrogen bonding may begin in different places for the interactions of a given strand with the one preceding it and the one following it in the sheet. Example 1 - simple beta-barrel. <PDBx:struct_sheet_hbondCategory> <PDBx:struct_sheet_hbond range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>11</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>19</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>30</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>40</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>31</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>39</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>50</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>60</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>51</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>59</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>70</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>80</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>71</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>89</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>90</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>100</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>91</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>99</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>110</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>120</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>111</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>119</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>130</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>140</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>131</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>139</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>150</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>160</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>151</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>159</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>10</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>180</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> </PDBx:struct_sheet_hbondCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. <PDBx:struct_sheet_hbondCategory> <PDBx:struct_sheet_hbond range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_2"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>20</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>18</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>119</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>111</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_2"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>110</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>N</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>118</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>33</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>O</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>41</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>38</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>40</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>52</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>50</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_c" range_id_2="strand_d2" sheet_id="sheet_2"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>30</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>36</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>96</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>90</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>51</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>51</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>80</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>80</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> <PDBx:struct_sheet_hbond range_id_1="strand_d2" range_id_2="strand_e" sheet_id="sheet_2"> <PDBx:range_1_beg_label_atom_id>N</PDBx:range_1_beg_label_atom_id> <PDBx:range_1_beg_label_seq_id>91</PDBx:range_1_beg_label_seq_id> <PDBx:range_1_end_label_atom_id>O</PDBx:range_1_end_label_atom_id> <PDBx:range_1_end_label_seq_id>97</PDBx:range_1_end_label_seq_id> <PDBx:range_2_beg_label_atom_id>O</PDBx:range_2_beg_label_atom_id> <PDBx:range_2_beg_label_seq_id>76</PDBx:range_2_beg_label_seq_id> <PDBx:range_2_end_label_atom_id>N</PDBx:range_2_end_label_atom_id> <PDBx:range_2_end_label_seq_id>70</PDBx:range_2_end_label_seq_id> </PDBx:struct_sheet_hbond> </PDBx:struct_sheet_hbondCategory> Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute auth_asym_id in category atom_site. Pointer to attribute auth_comp_id in category atom_site Pointer to attribute label_asym_id in category atom_site. Pointer to attribute label_comp_id in category atom_site Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute auth_comp_id in category atom_site. Pointer to attribute auth_comp_id in category atom_site. Pointer to attribute label_asym_id in category atom_site. Pointer to attribute label_comp_id in category atom_site. Pointer to attribute pdbx_PDB_ins_code in category atom_site. Pointer to attribute label_asym_id in category atom_site. Pointer to attribute label_comp_id in category atom_site. Pointer to attribute label_asym_id in category atom_site. Pointer to attribute label_comp_id in category atom_site. Place holder for PDB insertion code. A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the first partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the first partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the second partner of the first hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue for the second partner of the last hydrogen bond between two residue ranges in a sheet. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. Data items in the STRUCT_SHEET_ORDER category record details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet. These data items are an alternative to the STRUCT_SHEET_TOPOLOGY data items and they allow all manner of sheets to be described. Example 1 - simple beta-barrel. <PDBx:struct_sheet_orderCategory> <PDBx:struct_sheet_order range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> </PDBx:struct_sheet_orderCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. <PDBx:struct_sheet_orderCategory> <PDBx:struct_sheet_order range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_2"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_2"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_c" range_id_2="strand_d2" sheet_id="sheet_2"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_order> <PDBx:struct_sheet_order range_id_1="strand_d2" range_id_2="strand_e" sheet_id="sheet_2"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_order> </PDBx:struct_sheet_orderCategory> Designates the relative position in the sheet, plus or minus, of the second residue range to the first. A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. Data items in the STRUCT_SHEET_RANGE category record details about the residue ranges that form a beta-sheet. Residues are included in a range if they made beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range. Example 1 - simple beta-barrel. <PDBx:struct_sheet_rangeCategory> <PDBx:struct_sheet_range id="strand_a" sheet_id="sheet_1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>20</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>30</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_b" sheet_id="sheet_1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>40</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>50</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_c" sheet_id="sheet_1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>60</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>70</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_d" sheet_id="sheet_1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>80</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>90</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_e" sheet_id="sheet_1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>100</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>110</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_f" sheet_id="sheet_1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>120</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>130</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_g" sheet_id="sheet_1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>140</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>150</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_h" sheet_id="sheet_1"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>160</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>170</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> </PDBx:struct_sheet_rangeCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. <PDBx:struct_sheet_rangeCategory> <PDBx:struct_sheet_range id="strand_a" sheet_id="sheet_2"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>10</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>18</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_b" sheet_id="sheet_2"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>110</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>119</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_c" sheet_id="sheet_2"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>30</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>41</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_d1" sheet_id="sheet_2"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>50</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>52</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_d2" sheet_id="sheet_2"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>90</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>97</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> <PDBx:struct_sheet_range id="strand_e" sheet_id="sheet_2"> <PDBx:beg_label_asym_id>A</PDBx:beg_label_asym_id> <PDBx:beg_label_comp_id>ala</PDBx:beg_label_comp_id> <PDBx:beg_label_seq_id>70</PDBx:beg_label_seq_id> <PDBx:end_label_asym_id>A</PDBx:end_label_asym_id> <PDBx:end_label_comp_id>ala</PDBx:end_label_comp_id> <PDBx:end_label_seq_id>80</PDBx:end_label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_sheet_range> </PDBx:struct_sheet_rangeCategory> A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. A component of the identifier for the residue at which the beta-sheet range begins. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute id in category struct_asym in the STRUCT_ASYM category. A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute id in category chem_comp in the CHEM_COMP category. A component of the identifier for the residue at which the beta-sheet range ends. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. A component of the identifier for the residue at which the beta sheet range begins. Insertion code. A component of the identifier for the residue at which the beta sheet range ends. Insertion code. Describes the symmetry operation that should be applied to the residues delimited by the start and end designators in order to generate the appropriate strand in this sheet. The value of attribute id in category struct_sheet_range must uniquely identify a range in a given sheet in the STRUCT_SHEET_RANGE list. Note that this item need not be a number; it can be any unique identifier. This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. Data items in the STRUCT_SHEET_TOPOLOGY category record details about the topology of the residue ranges that form a beta-sheet. All topology links are pairwise and the specified pairs are assumed to be successive in the amino-acid sequence. These data items are useful in describing various simple and complex folds, but they become inadequate when the strands in the sheet come from more than one chain. The STRUCT_SHEET_ORDER data items can be used to describe single- and multiple-chain-containing sheets. Example 1 - simple beta-barrel. <PDBx:struct_sheet_topologyCategory> <PDBx:struct_sheet_topology range_id_1="strand_a" range_id_2="strand_b" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_b" range_id_2="strand_c" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_c" range_id_2="strand_d" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_d" range_id_2="strand_e" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_e" range_id_2="strand_f" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_f" range_id_2="strand_g" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_g" range_id_2="strand_h" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_h" range_id_2="strand_a" sheet_id="sheet_1"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>parallel</PDBx:sense> </PDBx:struct_sheet_topology> </PDBx:struct_sheet_topologyCategory> Example 2 - five stranded mixed-sense sheet with one two-piece strand. <PDBx:struct_sheet_topologyCategory> <PDBx:struct_sheet_topology range_id_1="strand_a" range_id_2="strand_c" sheet_id="sheet_2"> <PDBx:offset>+2</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_c" range_id_2="strand_d1" sheet_id="sheet_2"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_d1" range_id_2="strand_e" sheet_id="sheet_2"> <PDBx:offset>+1</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_e" range_id_2="strand_d2" sheet_id="sheet_2"> <PDBx:offset>-1</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_topology> <PDBx:struct_sheet_topology range_id_1="strand_d2" range_id_2="strand_b" sheet_id="sheet_2"> <PDBx:offset>-2</PDBx:offset> <PDBx:sense>anti-parallel</PDBx:sense> </PDBx:struct_sheet_topology> </PDBx:struct_sheet_topologyCategory> Designates the relative position in the sheet, plus or minus, of the second residue range to the first. A flag to indicate whether the two designated residue ranges are parallel or antiparallel to one another. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet_range in the STRUCT_SHEET_RANGE category. This data item is a pointer to attribute id in category struct_sheet in the STRUCT_SHEET category. Data items in the STRUCT_SITE category record details about portions of the structure that contribute to structurally relevant sites (e.g. active sites, substrate-binding subsites, metal-coordination sites). Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_siteCategory> <PDBx:struct_site id="P2 site C"> <PDBx:details> residues with a contact &lt; 3.7 \&#37;A to an atom in the P2 moiety of the inhibitor in the conformation with _struct_asym.id = C</PDBx:details> </PDBx:struct_site> <PDBx:struct_site id="P2 site D"> <PDBx:details> residues with a contact &lt; 3.7 \&#37;A to an atom in the P1 moiety of the inhibitor in the conformation with _struct_asym.id = D)</PDBx:details> </PDBx:struct_site> </PDBx:struct_siteCategory> A description of special aspects of the site. A component of the identifier for the ligand in the site. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for the ligand in the site. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. PDB insertion code for the ligand in the site. A component of the identifier for the ligand in the site. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. Source of evidence supporting the assignment of this site. SOFTWARE AUTHOR UNKNOWN Number of residues in the site. The value of attribute id in category struct_site must uniquely identify a record in the STRUCT_SITE list. Note that this item need not be a number; it can be any unique identifier. Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_site_genCategory> <PDBx:struct_site_gen id="1" site_id="1"> <PDBx:details xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>32</PDBx:label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_site_gen> <PDBx:struct_site_gen id="2" site_id="1"> <PDBx:details xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>47</PDBx:label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_site_gen> <PDBx:struct_site_gen id="3" site_id="1"> <PDBx:details xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>82</PDBx:label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_site_gen> <PDBx:struct_site_gen id="4" site_id="1"> <PDBx:details xsi:nil="true" /> <PDBx:label_asym_id>A</PDBx:label_asym_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>84</PDBx:label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_site_gen> <PDBx:struct_site_gen id="5" site_id="2"> <PDBx:details xsi:nil="true" /> <PDBx:label_asym_id>B</PDBx:label_asym_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>232</PDBx:label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_site_gen> <PDBx:struct_site_gen id="6" site_id="2"> <PDBx:details xsi:nil="true" /> <PDBx:label_asym_id>B</PDBx:label_asym_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>247</PDBx:label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_site_gen> <PDBx:struct_site_gen id="7" site_id="2"> <PDBx:details xsi:nil="true" /> <PDBx:label_asym_id>B</PDBx:label_asym_id> <PDBx:label_comp_id>VAL</PDBx:label_comp_id> <PDBx:label_seq_id>282</PDBx:label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_site_gen> <PDBx:struct_site_gen id="8" site_id="2"> <PDBx:details xsi:nil="true" /> <PDBx:label_asym_id>B</PDBx:label_asym_id> <PDBx:label_comp_id>ILE</PDBx:label_comp_id> <PDBx:label_seq_id>284</PDBx:label_seq_id> <PDBx:symmetry>1_555</PDBx:symmetry> </PDBx:struct_site_gen> </PDBx:struct_site_genCategory> A component of the identifier for participants in the site. This data item is a pointer to attribute auth_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute auth_atom_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute auth_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute auth_seq_id in category atom_site in the ATOM_SITE category. A description of special aspects of the symmetry generation of this portion of the structural site. The zinc atom lies on a special position; application of symmetry elements to generate the insulin hexamer will generate excess zinc atoms, which must be removed by hand. A component of the identifier for participants in the site. This data item is a pointer to attribute id in category atom_sites_alt in the ATOM_SITES_ALT category. A component of the identifier for participants in the site. This data item is a pointer to attribute label_asym_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute atom_id in category chem_comp_atom in the CHEM_COMP_ATOM category. A component of the identifier for participants in the site. This data item is a pointer to attribute label_comp_id in category atom_site in the ATOM_SITE category. A component of the identifier for participants in the site. This data item is a pointer to attribute label_seq_id in category atom_site in the ATOM_SITE category. PDB insertion code. Number of residues in the site. Describes the symmetry operation that should be applied to the atom set specified by attribute label* in category struct_site_gen to generate a portion of the site. 4th symmetry operation applied 4 7th symm. posn.; +a on x; -b on y 7_645 The value of attribute id in category struct_site_gen must uniquely identify a record in the STRUCT_SITE_GEN list. Note that this item need not be a number; it can be any unique identifier. This data item is a pointer to attribute id in category struct_site in the STRUCT_SITE category. Data items in the STRUCT_SITE_KEYWORDS category record keywords describing the site. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:struct_site_keywordsCategory> <PDBx:struct_site_keywords site_id="P2 site C" text="binding site"></PDBx:struct_site_keywords> <PDBx:struct_site_keywords site_id="P2 site C" text="binding pocket"></PDBx:struct_site_keywords> <PDBx:struct_site_keywords site_id="P2 site C" text="P2 site"></PDBx:struct_site_keywords> <PDBx:struct_site_keywords site_id="P2 site C" text="P2 pocket"></PDBx:struct_site_keywords> <PDBx:struct_site_keywords site_id="P2 site D" text="binding site"></PDBx:struct_site_keywords> <PDBx:struct_site_keywords site_id="P2 site D" text="binding pocket"></PDBx:struct_site_keywords> <PDBx:struct_site_keywords site_id="P2 site D" text="P2 site"></PDBx:struct_site_keywords> <PDBx:struct_site_keywords site_id="P2 site D" text="P2 pocket"></PDBx:struct_site_keywords> </PDBx:struct_site_keywordsCategory> This data item is a pointer to attribute id in category struct_site in the STRUCT_SITE category. Keywords describing this site. active site binding pocket Ca coordination Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site. Example 1 - based on NDB structure GDL001 by Coll, Aymami, Van Der Marel, Van Boom, Rich & Wang [Biochemistry (1989), 28, 310-320]. <PDBx:struct_site_viewCategory> <PDBx:struct_site_view id="1"> <PDBx:details> This view highlights the site of ATAT-Netropsin interaction.</PDBx:details> <PDBx:rot_matrix11>0.132</PDBx:rot_matrix11> <PDBx:rot_matrix12>0.922</PDBx:rot_matrix12> <PDBx:rot_matrix13>-0.363</PDBx:rot_matrix13> <PDBx:rot_matrix21>0.131</PDBx:rot_matrix21> <PDBx:rot_matrix22>-0.380</PDBx:rot_matrix22> <PDBx:rot_matrix23>-0.916</PDBx:rot_matrix23> <PDBx:rot_matrix31>-0.982</PDBx:rot_matrix31> <PDBx:rot_matrix32>0.073</PDBx:rot_matrix32> <PDBx:rot_matrix33>-0.172</PDBx:rot_matrix33> </PDBx:struct_site_view> </PDBx:struct_site_viewCategory> A description of special aspects of this view of the site. This data item can be used as a figure legend. The active site has been oriented with the specificity pocket on the right and the active site machinery on the left. The [1][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [1][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [1][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [2][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [2][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [2][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [3][1] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [3][2] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category to an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| The [3][3] element of the matrix used to rotate the subset of the Cartesian coordinates in the ATOM_SITE category identified in the STRUCT_SITE_GEN category an orientation useful for visualizing the site. The conventions used in the rotation are described in attribute details. in category struct_site_view |x'| |11 12 13| |x| |y'|~reoriented Cartesian~ = |21 22 23| |y|~Cartesian~ |z'| |31 32 33| |z| This data item is a pointer to attribute id in category struct_site in the STRUCT_SITE category. The value of attribute id in category struct_site_view must uniquely identify a record in the STRUCT_SITE_VIEW list. Note that this item need not be a number; it can be any unique identifier. Figure 1 unliganded enzyme view down enzyme active site Data items in the SYMMETRY category record details about the space-group symmetry. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:symmetryCategory> <PDBx:symmetry entry_id="5HVP"> <PDBx:Int_Tables_number>18</PDBx:Int_Tables_number> <PDBx:cell_setting>orthorhombic</PDBx:cell_setting> <PDBx:space_group_name_H-M>P 21 21 2</PDBx:space_group_name_H-M> </PDBx:symmetry> </PDBx:symmetryCategory> Space-group number from International Tables for Crystallography Vol. A (2002). The cell settings for this space-group symmetry. Used for PDB space group: Example: 'C 1 2 1' (instead of C 2) 'P 1 2 1' (instead of P 2) 'P 1 21 1' (instead of P 21) 'P 1 1 21' (instead of P 21 -unique C axis) 'H 3' (instead of R 3 -hexagonal) 'H 3 2' (instead of R 3 2 -hexagonal) Example: 'C 1 2 1' (instead of C 2) 'P 1 2 1' (instead of P 2) 'P 1 21 1' (instead of P 21) 'P 1 1 21' (instead of P 21 -unique C axis) 'H 3' (instead of R 3 -hexagonal) 'H 3 2' (instead of R 3 2 -hexagonal) Hermann-Mauguin space-group symbol. Note that the Hermann-Mauguin symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used, always supply the FULL symbol from International Tables for Crystallography Vol. A (2002) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol, specify the attribute pos_as_xyz in category symmetry_equiv or attribute space_group_name_Hall in category symmetry data items as well. Leave spaces between symbols referring to different axes. A 1 A 1 2 1 A 2 B 1 1 2 B 2 B 2 21 2 C 2 C 1 2 1 C 21 C 1 21 1 C 2(A 112) C 2 2 2 C 2 2 21 C 4 21 2 F 2 2 2 F 2 3 F 4 2 2 F 4 3 2 F 41 3 2 I 1 2 1 I 1 21 1 I 2 I 2 2 2 I 2 3 I 21 I 21 3 I 21 21 21 I 4 I 4 2 2 I 4 3 2 I 41 I 41/a I 41 2 2 I 41 3 2 P 1 P 1- P 2 P 1 2 1 P 1 1 2 P 2 2 2 P 2 3 P 2 2 21 P 2 21 21 P 21 P 1 21 1 P 1 21/c 1 P 1 1 21 P 21(C) P 21 2 21 P 21 3 P 21 21 2 P 21 21 2 A P 21 21 21 P 3 P 3 1 2 P 3 2 1 P 31 P 31 1 2 P 31 2 1 P 32 P 32 1 2 P 32 2 1 P 4 P 4 2 2 P 4 3 2 P 4 21 2 P 41 P 41 2 2 P 41 3 2 P 41 21 2 P 42 P 42 2 2 P 42 3 2 P 42 21 2 P 43 P 43 2 2 P 43 3 2 P 43 21 2 P 6 P 6 2 2 P 61 P 61 2 2 P 62 P 62 2 2 P 63 P 63 2 2 P 64 P 64 2 2 P 65 P 65 2 2 H 3 R 3 H 3 2 R 3 2 Space-group symbol as described by Hall (1981). This symbol gives the space-group setting explicitly. Leave spaces between the separate components of the symbol. Ref: Hall, S. R. (1981). Acta Cryst. A37, 517-525; erratum (1981) A37, 921. -P 2ac 2n -R 3 2" P 61 2 2 (0 0 -1) This data item is a pointer to attribute id in category entry in the ENTRY category. Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group. Example 1 - based on PDB entry 5HVP and laboratory records for the structure corresponding to PDB entry 5HVP. <PDBx:symmetry_equivCategory> <PDBx:symmetry_equiv id="1"> <PDBx:pos_as_xyz>+x,+y,+z</PDBx:pos_as_xyz> </PDBx:symmetry_equiv> <PDBx:symmetry_equiv id="2"> <PDBx:pos_as_xyz>-x,-y,z</PDBx:pos_as_xyz> </PDBx:symmetry_equiv> <PDBx:symmetry_equiv id="3"> <PDBx:pos_as_xyz>1/2+x,1/2-y,-z</PDBx:pos_as_xyz> </PDBx:symmetry_equiv> <PDBx:symmetry_equiv id="4"> <PDBx:pos_as_xyz>1/2-x,1/2+y,-z</PDBx:pos_as_xyz> </PDBx:symmetry_equiv> </PDBx:symmetry_equivCategory> Symmetry-equivalent position in the 'xyz' representation. Except for the space group P1, these data will be repeated in a loop. The format of the data item is as per International Tables for Crystallography Vol. A (2002). All equivalent positions should be entered, including those for lattice centring and a centre of symmetry, if present. -y+x,-y,1/3+z The value of attribute id in category symmetry_equiv must uniquely identify a record in the SYMMETRY_EQUIV category. Note that this item need not be a number; it can be any unique identifier. Data items in the VALENCE_PARAM category define the parameters used for calculating bond valences from bond lengths. In addition to the parameters, a pointer is given to the reference (in VALENCE_REF) from which the bond-valence parameters were taken. Example 1 - a bond-valence parameter list with accompanying references. <PDBx:valence_paramCategory> <PDBx:valence_param atom_1="Cu" atom_1_valence="2" atom_2="O" atom_2_valence="-2"> <PDBx:B>0.37</PDBx:B> <PDBx:Ro>1.679</PDBx:Ro> <PDBx:details xsi:nil="true" /> <PDBx:ref_id>a</PDBx:ref_id> </PDBx:valence_param> <PDBx:valence_param atom_1="Cu" atom_1_valence="2" atom_2="O" atom_2_valence="-2"> <PDBx:B>0.37</PDBx:B> <PDBx:Ro>1.649</PDBx:Ro> <PDBx:details xsi:nil="true" /> <PDBx:ref_id>j</PDBx:ref_id> </PDBx:valence_param> <PDBx:valence_param atom_1="Cu" atom_1_valence="2" atom_2="N" atom_2_valence="-3"> <PDBx:B>0.37</PDBx:B> <PDBx:Ro>1.64</PDBx:Ro> <PDBx:details>2-coordinate N</PDBx:details> <PDBx:ref_id>m</PDBx:ref_id> </PDBx:valence_param> <PDBx:valence_param atom_1="Cu" atom_1_valence="2" atom_2="N" atom_2_valence="-3"> <PDBx:B>0.37</PDBx:B> <PDBx:Ro>1.76</PDBx:Ro> <PDBx:details>3-coordinate N</PDBx:details> <PDBx:ref_id>m</PDBx:ref_id> </PDBx:valence_param> </PDBx:valence_paramCategory> <PDBx:valence_refCategory> <PDBx:valence_ref id="a"> <PDBx:reference>Brown &amp; Altermatt (1985), Acta Cryst. B41, 244-247</PDBx:reference> </PDBx:valence_ref> <PDBx:valence_ref id="j"> <PDBx:reference>Liu &amp; Thorp (1993), Inorg. Chem. 32, 4102-4205</PDBx:reference> </PDBx:valence_ref> <PDBx:valence_ref id="m"> <PDBx:reference>See, Krause &amp; Strub (1998), Inorg. Chem. 37, 5369-5375</PDBx:reference> </PDBx:valence_ref> </PDBx:valence_refCategory> The bond-valence parameter B used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R. The bond-valence parameter Ro used in the expression s = exp[(Ro - R)/B] where s is the valence of a bond of length R. Details of or comments on the bond-valence parameters. An identifier for the valence parameters of a bond between the given atoms. An identifier which links to the reference to the source from which the bond-valence parameters are taken. A child of attribute id in category valence_ref which it must match. The element symbol of the first atom forming the bond whose bond-valence parameters are given in this category. The valence (formal charge) of the first atom whose bond-valence parameters are given in this category. The element symbol of the second atom forming the bond whose bond-valence parameters are given in this category. The valence (formal charge) of the second atom whose bond-valence parameters are given in this category. Data items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken. Literature reference from which the valence parameters identified by attribute id in category valence_param were taken. An identifier for items in this category. Parent of attribute ref_id in category valence_param, which must have the same value.