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.