 | ||
| © RCSB PDB | ||
DATA ITEMS RECOMMENDED FOR DEPOSITING CRYSTALLOGRAPHIC STRUCTURE
DETERMINATIONS
(Revised:
05-Oct-2002)
Please
email jwest@rcsb.rutgers.edu with any comments/questions on these items.
Further
details are
available from http://mmcif.rcsb.org
(Status items:
PDB=Currently in PDB
mmCIF=defined in PDB exchange data dictionary)
MOLECULAR INFORMATION:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Macromolecules |
|
|
|
|
Molecule
name |
_entity.pdbx_description
holds the name corresponding to PDB compound name. Multiple
systematic and common names can be supplied in mmCIF categories entity_name_sys
and entity_name_com |
PDB,mmCIF |
|
|
Sequence
(one-letter code) |
_entity_poly.pdbx_seq_one_letter_code |
PDB,mmCIF |
|
|
Fragment |
_entity.pdbx_fragment |
PDB,mmCIF |
|
|
Mutations |
_entity.pdbx_mutation |
PDB,mmCIF |
|
|
Modifications
(e.g. chemical or post-translational modifications) |
_entity.pdbx_modification |
mmCIF |
|
|
Experimental
Mass |
_entity.pdbx_formula_weight_exptl _entity.pdbx_formula_weight_exptl_meth |
mmCIF |
|
|
E.C.
number |
_entity.pdbx_ec |
PDB,mmCIF |
|
|
Non-polymers |
|
|
|
|
Molecule
name |
_chem_comp.name |
PDB,mmCIF |
|
|
Molecular
topology |
mmCIF
categories chem_comp_atom and chem_comp_bond for any non-polymer molecules
not describe in the PDB ligand dictionary. |
PDB,mmCIF |
|
Notes: Macromolecule names are recorded in PDB
COMPND records. All of the above items
are included in the current format. The
assignment of multiple common and systematic names is supported by mmCIF but
not in the PDB format.
CRYSTALLIZATION
CONDITIONS AND UNIT CELL PARAMETERS:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Crystallization
method |
_exptl_crystal_grow.method |
PDB,mmCIF |
|
|
Apparatus |
_exptl_crystal_grow.apparatus |
PDB,mmCIF |
|
|
Temperature |
_exptl_crystal_grow.temp _exptl_crystal_grow.temp_details |
PDB,mmCIF |
|
|
pH |
_exptl_crystal_grow.pH _exptl_crystal_grow.pdbx_pH_range |
PDB,mmCIF |
|
|
Crystallization
solutions compositions |
Tabulated
in mmCIF category exptl_crystal_grow_comp |
PDB,mmCIF |
|
|
Additional
treatments (e.g. soaking, time in drop, annealing, cryoprotectant, etc) |
_exptl_crystal.preparation |
PDB,mmCIF |
|
|
Image
of crystal |
_exptl_crystal.pdbx_crystal_image_url _exptl_crystal.pdbx_crystal_image_format |
mmCIF |
|
|
Crystal
size |
_exptl_crystal.size_* |
mmCIF |
|
|
Cell
constants |
_cell.length_a _cell.length_b _cell.length_c _cell.length_alpha _cell.length_beta _cell.length_gamma |
PDB,mmCIF |
|
|
ESD
of Cell constants |
_cell.length_a_esd _cell.length_b_esd _cell.length_c_esd _cell.length_alpha_esd _cell.length_beta_esd _cell.length_gamma_esd |
mmCIF |
|
|
Space
Group |
_symmetry.space_group_name_H-M |
PDB,mmCIF |
|
Notes: Crystallization conditions are recorded as
free text in PDB REMARK 280. Cell constants are recorded on the PDB CRYST1
records. mmCIF provides for description
of multiple crystals and maintains the correspondences between each crystal and
its associated diffraction data sets.
SOURCE
INFORMATION:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Organism
common name |
_entity_src_gen.gene_src_common_name |
PDB,mmCIF |
|
|
Organism
scientific name |
_entity_src_gen.pdbx_gene_src_scientific_name |
PDB,mmCIF |
|
|
Organ |
_entity_src_gen.pdbx_gene_src_organ |
PDB,mmCIF |
|
|
Gene |
_entity_src_gen.pdbx_gene_src_gene
|
PDB,mmCIF |
|
|
Cellular
location |
_entity_src_gen.pdbx_gene_src_cellular_location |
PDB,mmCIF |
|
|
|
|
|
|
|
Expression
system common name |
_entity_src_gen.host_org_common_name |
PDB,mmCIF |
|
|
Expression
system scientific name |
_entity_src_gen.pdbx_host_org_scientific_name |
PDB,mmCIF |
|
|
Expression
system cell line |
_entity_src_gen.pdbx_host_org_cell_line |
PDB,mmCIF |
|
|
Expression
system strain |
_entity_src_gen.pdbx_host_org_strain |
PDB,mmCIF |
|
|
Expression
system variant |
_entity_src_gen.pdbx_host_org_variant
|
PDB,mmCIF |
|
|
Expression
vector |
_entity_src_gen.pdbx_host_org_vector |
PDB,mmCIF |
|
|
Expression
plasmid |
_entity_src_gen.plasmid_name
|
PDB,mmCIF |
|
|
Expression
system cellular location |
_entity_src_gen.pdbx_host_org_cellular_location |
PDB,mmCIF |
|
|
Expression
system gene |
_entity_src_gen.pdbx_host_org_gene |
PDB,mmCIF |
|
Notes: Source information is recorded in PDB
SOURCE records. All of the above
source items are represented in the current format. Source information is greatly expanded in the recommendations for
deposition of protein production data.
DATA
COLLECTION DESCRIPTION AND STATISTICS:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Data
collection date |
_diffrn_detector.pdbx_collection_date |
mmCIF |
|
|
Data
collection site |
_diffrn_source.pdbx_synchrotron_site |
PDB,mmCIF |
|
|
Beamline |
_diffrn_source.pdbx_synchrotron_beamline |
PDB,mmCIF |
|
|
Detector |
_diffrn_detector.detector _diffrn_detector.type |
PDB,mmCIF |
|
|
Collection
temperature |
_diffrn.ambient_temp _diffrn.ambient_temp_details |
PDB,mmCIF |
|
|
Total
unique reflections collected |
_reflns.number_all |
PDB,mmCIF |
|
|
Observed
reflections (> Sigma cutoff) |
_reflns.number_obs |
mmCIF |
|
|
Criterion
for “observed” reflections |
_reflns.observed_criterion |
PDB,mmCIF |
|
|
Wavelength(s)
used (simplified) |
_diffrn_radiation.pdbx_wavelength_list |
PDB,mmCIF |
|
|
Wavelength(s)
used (detailed) |
_diffrn_radiation_wavelength.wavelength |
PDB,mmCIF |
|
|
Resolution
range |
_reflns.d_resolution_high _reflns.d_resolution_low
|
PDB,mmCIF |
|
|
Reflections
rejected in scaling |
_reflns.pdbx_scaling_rejects |
mmCIF |
|
|
Completeness
(observed) |
_reflns.percent_possible_obs |
PDB,mmCIF |
|
|
Completeness
of high resolution shells |
_reflns_shell.percent_possible_obs |
PDB,mmCIF |
|
|
Completeness
of all resolution shells |
_reflns_shell.percent_possible_obs |
mmCIF |
|
|
Redundancy
overall |
_reflns.pdbx_redundancy |
PDB,mmCIF |
|
|
Redundancy
for high resolution shell |
_reflns_shell.pdbx_redundancy |
PDB,mmCIF |
|
|
Redundancy
(all resolution shells) |
_reflns_shell.pdbx_redundancy |
mmCIF |
|
|
R-Merge
(overall observed) |
_reflns.Rmerge_F_obs _reflns.pdbx_Rmerge_I_obs |
PDB,mmCIF |
|
|
R-Merge
(high resolution shell) |
_reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_obs |
PDB,mmCIF |
|
|
R-Merge
(all resolution shells) |
_reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_obs |
mmCIF |
|
|
R-Sym
(overall observed) |
_reflns.pdbx_Rsym_value |
PDB,mmCIF |
|
|
R-Meas
(Deidrichs and Karplus) |
_reflns.pdbx_Rmeas_value |
mmCIF |
|
|
R-Sym
(high resolution shell) |
_reflns_shell.pdbx_Rsym_value |
PDB,mmCIF |
|
|
R-Sym
(all resolution shells) |
_reflns_shell.pdbx_Rsym_value |
mmCIF,O |
|
|
<I>
over <sigma I> (overall observed) |
_reflns_shell.meanI_over_sigI |
PDB,mmCIF |
|
|
<I>
over <sigma I> (high
resolution shell) |
_reflns_shell.meanI_over_sigI |
PDB,mmCIF |
|
|
<I>
over <sigma I> (all
resolution shells) |
_reflns_shell.meanI_over_sigI |
mmCIF |
|
|
Chi-squared
overall |
_reflns.pdbx_chi_squared |
mmCIF |
|
|
Chi-squared
(all resolution shells) |
_reflns_shell.pdbx_chi_squared |
mmCIF |
|
|
Optical
resolution (i.e. determined by SFCHECK) |
_reflns.pdbx_d_res_high_opt _reflns.pdbx_d_res_low_opt _reflns.pdbx_d_res_opt_method |
mmCIF |
|
|
Data
processing software |
mmCIF
category “software” provides for complete
program description. |
PDB,mmCIF |
|
Notes: Data collection details are recorded in PDB
REMARK 200. The description above
provides a summary of the collected data with respect to the solved structure.
DATA
COLLECTION - EXPERIMENTAL INTENSITY DATA:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Miller
index h |
_refln.index_h |
mmCIF |
|
|
Miller
index k |
_refln.index_k |
mmCIF |
|
|
Miller
index l |
_refln.index_l |
mmCIF |
|
|
Intensity
(measured) |
_refln.intensity_meas |
mmCIF |
|
|
Intensity
standard uncertainty
(measured) |
_refln.intensity_sigma |
mmCIF |
|
|
Geometry |
imgCIF
category diffrn_scan, diffrn_scan_axis, diffrn_scan_frame, and
diffrn_scan_frame_axis provide detailed collection geometry information. |
imgCIF |
|
|
Time
collected |
imgCIF
category diffrn_scan contains detailed timing information |
imgCIF |
|
Notes:
This section should capture all information required to remerge and rescale the
observed intensity data. The geometry of each observation needs to be recorded
(rotation, detector position etc.).
Many of the data collection details are described in the imgCIF
dictionary.
DATA
COLLECTION - EXPERIMENTAL AMPLITUDE DATA:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Miller
index h |
_refln.index_h |
PDB,mmCIF |
|
|
Miller
index k |
_refln.index_k |
PDB,mmCIF |
|
|
Miller
index l |
_refln.index_l |
PDB,mmCIF |
|
|
Structure
factor (meausured) |
_refln.F_meas_au |
PDB,mmCIF |
|
|
Structure
factor standard uncertainty
(measured) |
_refln.F_meas_sigma_au |
PDB,mmCIF |
|
|
Classification
of reflection in refinement (e.g.
working set, cross-validation set) |
_refln.status |
PDB,mmCIF |
|
Notes:
It is recommended that the above data items be deposited for each data set
contributing to the deposited structure.
Data should be deposited in unscaled and unmerged form as well as the
final merged and scaled data used in refinement. If the data are originally encoded in imgCIF/CBF, then much
greater detail is available describing the diffraction data sets that
contributes to the final merged data set.
STRUCTURE
SOLUTION AND PHASING:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
For
each MAD or SAD data set: |
|
|
|
|
Wavelength |
_phasing_MAD_set.wavelength |
mmCIF |
|
|
Resolution range |
_phasing_MAD_set.d_res_high _phasing_MAD_set.d_res_low |
mmCIF |
|
|
Number of sites |
_phasing_MAD_set.number_of_sites |
mmCIF |
|
|
|
|
|
|
|
Anomalous site identities |
_phasing_MAD_set_site.id |
mmCIF |
|
|
Anomalous site positions |
_phasing_MAD_set_site.Cartn_x _phasing_MAD_set_site.Cartn_y _phasing_MAD_set_site.Cartn_z |
mmCIF |
|
|
Anomalous site B-factors (isotropic) |
_phasing_MAD_set_site.B_iso |
mmCIF |
|
|
Anomalous site B-factors (anisotropic) |
_phasing_MAD_set_site.aniso_B[][] |
mmCIF |
|
|
Anomalous site occupancies |
_phasing_MAD_set_site.occupancy |
mmCIF |
|
|
|
|
|
|
|
f’
(experimental) |
_phasing_MAD_set.f_prime |
mmCIF |
|
|
f’’ (experimental) |
_phasing_MAD_set.f_double_prime |
mmCIF |
|
|
f’
(refined) |
_phasing_MAD_set.f_prime_refined |
mmCIF |
|
|
f’’ (refined) |
_phasing_MAD_set.f_double_prime_refined |
mmCIF
|
|
|
<FOM>
(overall) |
_phasing_MAD_expt.mean_fom |
mmCIF |
|
|
<FOM>
(resolution shells) |
_pdbx_phasing_MAD_expt_shell.pdbx_mean_fom |
mmCIF |
|
|
R-Cullis
(acentric) (overall) |
_phasing_MAD_expt.pdbx_R_Cullis_acentric |
mmCIF |
|
|
R-Cullis
(acentric) (resolution
shells) |
_pdbx_phasing_MAD_expt_shell.R_Cullis_acentric |
mmCIF |
|
|
R-Cullis
(centric) (overall) |
_phasing_MAD_expt.pdbx_R_Cullis_centric |
mmCIF |
|
|
R-Cullis
(centric) (resolution
shells) |
_pdbx_phasing_MAD_expt_shell.R_Cullis_centric |
mmCIF |
|
|
R-Cullis
(anomalous)(overall) |
_phasing_MAD_expt.pdbx_R_Cullis_anomalous |
mmCIF |
|
|
R-Cullis
(anomalous) (resolution
shells) |
_pdbx_phasing_MAD_expt_shell.R_Cullis_anomalous |
mmCIF |
|
|
R-Kraut
(centric) (overall) |
_phasing_MAD_expt.pdbx_R_Kraut_centric |
mmCIF |
|
|
R-Kraut
(acentric) (overall) |
_phasing_MAD_expt.pdbx_R_Kraut_acentric |
mmCIF |
|
|
Phasing
power (acentric) (overall) |
_phasing_MAD_expt.pdbx_power_acentric |
mmCIF |
|
|
Phasing
power (acentric) (resolution shells) |
_pdbx_phasing_MAD_expt_shell.power_acentric |
mmCIF |
|
|
Phasing
power (centric) (overall) |
_phasing_MAD_expt.pdbx_power_centric |
mmCIF |
|
|
Phasing
power (centric) (resolution
shells) |
_pdbx_phasing_MAD_expt_shell.power_centric |
mmCIF |
|
Notes: The details of MAD
are not captured in the current PDB data file.
For SAD experiments the data item names are changed from MAD -> SAD.
STRUCTURE SOLUTION AND PHASING (continued):
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
For
each MIR or SIR data set: |
|
|
|
|
Resolution range |
_phasing_MIR_der.d_res_high _phasing_MIR_der.d_res_low |
mmCIF |
|
|
Number of sites |
_phasing_MIR_der.number_of_sites |
mmCIF |
|
|
Heavy atom location method |
_phasing_MIR.method |
mmCIF |
|
|
Heavy atom identities |
_phasing_MIR_der_site.id |
mmCIF |
|
|
Heavy atom positions |
_phasing_MIR_der_site.Cartn_x _phasing_MIR_der_site.Cartn_y _phasing_MIR_der_site.Cartn_z |
mmCIF |
|
|
Heavy atom B-factors |
_phasing_MIR_der_site.B_iso |
mmCIF |
|
|
Heavy atom occupancies |
_phasing_MIR_der_site.occupancy |
mmCIF |
|
|
Power acentric (overall) |
_phasing_MIR_der.power_acentric |
mmCIF |
|
|
Power acentric (resolution shells) |
_phasing_MIR_der_shell.pdbx_power_acentric |
mmCIF |
|
|
Power centric (overall) |
_phasing_MIR_der.power_centric |
mmCIF |
|
|
Power centric (resolution shells) |
_phasing_MIR_der_shell.pdbx_power_centric |
mmCIF |
|
|
R-Cullis (acentric) (overall) |
_phasing_MIR_der.R_Cullis_acentric |
mmCIF |
|
|
R-Cullis (acentric) (resolution shells) |
_phasing_MIR_der_shell._pdbx_R_Cullis_acentric |
mmCIF |
|
|
R-Cullis (centric) (overall) |
_phasing_MIR_der.R_Cullis_centric |
mmCIF |
|
|
R-Cullis (centric) (resolution shells) |
_phasing_MIR_der_shell.pdbx_R_Cullis_centric |
mmCIF |
|
|
R-Cullis (anomalous) (overall) |
_phasing_MIR_der.R_Cullis_anomalous |
mmCIF |
|
|
R-Cullis (anomalous) (resolution shells) |
_phasing_MIR_der_shell.pdbx_R_Cullis_anomalous |
mmCIF |
|
|
R-Kraut (centric) (overall) |
_phasing_MIR_expt.pdbx_R_Kraut_centric |
mmCIF |
|
|
R-Kraut (acentric) (overall) |
_phasing_MIR_expt.pdbx_R_Kraut_acentric |
mmCIF |
|
|
<FOM> (overall) |
_phasing_MIR.FOM |
mmCIF |
|
|
<FOM> (high resolution shell) |
_phasing_MIR_der_shell.fom |
mmCIF |
|
|
<FOM> (all resolution shell) |
_phasing_MIR_der_shell.fom |
mmCIF |
|
|
|
|
|
|
|
Structure
solution software |
mmCIF
category “software” provides for complete
program description. |
mmCIF |
|
Notes: The details of MIR are not captured in the
current PDB data file. For SIR
experiments the data item names are changed from MIR -> SIR.
STRUCTURE SOLUTION AND PHASING (continued):
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
For
each MR data set: |
|
|
|
|
Resolution range |
_pdbx_phasing_MR.d_res_high _pdbx_phasing_MR.d_res_low |
mmCIF |
|
|
Criterion on sigma F/I |
_pdbx_phasing_MR.sigma_F _pdbx_phasing_MR.sigma_I |
mmCIF |
|
|
Outlier removal details |
_pdbx_phasing_MR.outlier_removal_details |
mmCIF |
|
|
Correlation of I/F(obs) to I/F(calc) for complete MR model |
_pdbx_phasing_MR.correlation_coeff_Io_to_Ic _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc |
mmCIF |
|
|
R-rigid (after rigid body refinement) |
_pdbx_phasing_MR.R_rigid_body |
mmCIF |
|
|
Starting model details |
_pdbx_phasing_MR.model_details |
mmCIF |
|
|
Coordinates
for each MR search fragment |
Deposit
each fragment coordinates set in an atom_site category in separate data
blocks. |
mmCIF |
|
|
Structure
solution software |
mmCIF
category “software” provides for complete
program description. |
mmCIF |
|
STRUCTURE SOLUTION AND PHASING (continued):
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Density
modification method |
_pdbx_phasing_DM.method
|
mmCIF |
|
|
Density
mod. mask type |
_pdbx_phasing_DM.mask_type |
mmCIF |
|
|
Density
mod. delta phi initial (overall) |
_pdbx_phasing_DM.delta_phi_initial |
mmCIF |
|
|
Density
mod. delta phi initial (shells) |
_pdbx_phasing_DM_shell.delta_phi_initial |
mmCIF |
|
|
Density
mod. delta phi final (overall) |
_pdbx_phasing_DM.delta_phi_final |
mmCIF |
|
|
Density
mod. delta phi final (shells) |
_pdbx_phasing_DM_shell.delta_phi_final |
mmCIF |
|
|
FOM
after density modification (overall) |
_pdbx_phasing_DM.fom |
mmCIF |
|
|
FOM
after density modification (resolution
shells) |
_pdbx_phasing_DM_shell.fom |
mmCIF |
|
|
NCS
mask determination method |
_pdbx_phasing_DM.ncs_mask_method |
mmCIF |
|
|
Structure
solution software |
mmCIF
category “software” provides for complete
program description. |
mmCIF |
|
|
|
|
|
|
MODEL BUILDING:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Model
building method |
_pdbx_model_building.method |
mmCIF |
|
|
Number
of building cycles |
_pdbx_model_building.num_cycles |
mmCIF |
|
|
Number
of atoms built |
_pdbx_model_building.num_atoms_built |
mmCIF |
|
|
Fraction
of expected side chains built |
_pdbx_model_building.frac_side_chains_built |
mmCIF |
|
|
Number
of chains built |
_pdbx_model_building.num_chains_built |
mmCIF |
|
|
arp/warp
connectivity index in first and last cycle |
_pdbx_model_building.arp_warp_connect_index_beg
_pdbx_model_building.arp_warp_connect_index_end |
mmCIF |
|
|
R-factor
prior to refinement |
_pdbx_model_building.R_factor_prerefine |
mmCIF |
|
|
free
R-factor prior to refinement |
_pdbx_model_building.R_factor_R_free_prerefine |
mmCIF |
|
|
Density
correlation between model and map |
_pdbx_model_building.correl_coeff_fo_to_fc |
mmCIF |
|
|
RMSD
of NCS related atoms |
_pdbx_model_building.rms_dev_position_ncs |
mmCIF |
|
|
Model
building software |
mmCIF
category “software” provides for complete
program description. |
mmCIF |
|
REFINEMENT
INFORMATION:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Resolution
range |
_refine.ls_d_res_low _refine.ls_d_res_high |
PDB,mmCIF |
|
|
Resolution
range (highest res. shell) |
_refine_ls_shell.d_res_low _refine_ls_shell.d_res_high |
PDB,mmCIF |
|
|
|
|
|
|
|
Number
of reflections used in refinement |
_refine.ls_number_reflns_obs |
PDB,mmCIF |
|
|
Number
of reflections in R-Free set |
_refine.ls_number_reflns_R_free |
PDB,mmCIF |
|
|
R-factor
(overall) |
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free |
PDB,mmCIF |
|
|
R-factor
(resolution
shells) |
_refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free |
mmCIF |
|
|
Number
of atoms refined |
_refine_hist.number_atoms_total _refine_hist.number_atoms_solvent _refine_hist.pdbx_number_atoms_protein _refine_hist.pdbx_number_atoms_nucleic_acid _refine_hist.pdbx_number_atoms_ligand |
PDB,mmCIF |
|
|
Number
of atoms refined (Other
atom types like lipid, carbohydrate,…) |
_refine_hist.pdbx_number_atoms_lipid _refine_hist.pdbx_number_atoms_carb |
mmCIF |
|
|
RMS
Bond Distances |
_refine_ls_restr.type _refine_ls_restr.dev_ideal_target _refine_ls_restr.dev_ideal |
PDB,mmCIF |
|
|
RMS
Bond Angles |
|||
|
RMS
Chiral Volume |
|||
|
RMS
Planar Torsion Angles |
|||
|
RMS
Staggered Torsion Angles |
|||
|
RMS
Orthonormal Torsion Angles |
|||
|
|
|
|
|
|
Isotropic
temperature factor restraints |
_refine_b_iso.class
_refine_b_iso.treatment _refine_b_iso.value |
PDB,mmCIF |
|
|
TLS
restraints |
mmCIF
categories pdbx_refine_tls and pdbx_refine_tls_group |
PDB,mmCIF |
|
|
Non-crystallographic
symmetry restraints |
NCS
related domains are described in mmCIF categories struct_ncs_dom and
struct_ncs_dom_lim. The
ncs operations relating the domain ensembles are described in categories
struct_ncs_ens, struct_ncs_ens_gen, and struct_ncs_oper. NCS restraints used in refinement are
described in category
refine_ls_restr_ncs. |
PDB,mmCIF |
|
|
Solvent
model used |
_refine.solvent_model_details _refine.solvent_model_param_bsol _refine.solvent_model_param_ksol |
PDB,mmCIF |
|
|
Starting
model |
_refine.pdbx_starting_model |
PDB,mmCIF |
|
|
Overall
Isotropic B Factor |
_refine.B_iso_mean |
PDB,mmCIF |
|
|
Overall
Anisotropic B Factor |
_refine.aniso_B[1][1] _refine.aniso_B[1][2] _refine.aniso_B[1][3] _refine.aniso_B[2][2] _refine.aniso_B[2][3] _refine.aniso_B[3][3] |
PDB,mmCIF |
|
|
Average
Isotropic B Factor + main chain atoms + side chain atoms + ligand atoms + solvent |
Computed
from _atom_site.B_iso_or_equiv |
PDB,mmCIF |
|
|
Topology/parameter
data used to refine deposited model |
_pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_refine_aux_file.file_name _pdbx_refine_aux_file.file_type |
mmCIF |
|
|
Identify
"pseudo-atoms" used to model unexplained density |
_refine_hist.pdbx_pseduo_atom_details |
mmCIF |
|
|
Refinement
software |
mmCIF
category “software” provides for complete
program description. |
PDB,mmCIF |
|
|
Stereochemical
Quality/ Ramachandran
analysis: + number of residues in favored regions + number of residues in additionally allowed regions + number of residues in generously allowed regions + number of residues in disallowed regions |
Currently
reported as part of validation protocols but not deposited or recorded in
data files. |
|
|
|
Real
space measure of fit by residue |
Currently
reported as part of validation protocols but not deposited or recorded in
data files. |
|
|
Notes: Refinement details are recorded in PDB
REMARK 3. All of the above refinement parameters, accept the
Ramachandran analysis, are included in the current PDB format file. Matrices describing NCS operations are
recorded in PDB MTRIX records.
REFINEMENT
SOLVENT MODEL AND MODEL STRUCTURE FACTOR INFORMATION:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Miller
index h |
_refln.index_h |
PDB,mmCIF |
|
|
Miller
index k |
_refln.index_k |
PDB,mmCIF |
|
|
Miller
index l |
_refln.index_l |
PDB,mmCIF |
|
|
Structure
factor amplitude arising from solvent model |
_refln.pdbx_F_calc_part_solvent |
PDB,mmCIF |
|
|
Structure
factor phase arising from solvent model |
_refln.pdbx_phase_calc_part_solvent |
PDB,mmCIF |
|
|
Structure
factor amplitude from final model including bulk solvent correction |
_refln.pdbx_F_calc_with_solvent |
PDB,mmCIF |
|
|
Structure
factor phase from final model including bulk solvent correction |
_refln.pdbx_phase_calc_with_solvent |
PDB,mmCIF |
|
MODEL
COORDINATES AND RELATED INFORMATION:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Atomic
coordinates, occupancies, and temperature factors |
mmCIF
category atom_site |
PDB,mmCIF |
|
|
Secondary
structure assignments |
mmCIF
categories struct_conf, struct_conf_type, struct_sheet_*,
pdbx_struct_sheet_hbond |
PDB,mmCIF |
|
|
Disulfide
bonds, hydrogen bonds, and salt bridges |
mmCIF
categories struct_conn and struct_conn_type |
PDB,mmCIF |
|
|
Biological
assembly description (if known) |
mmCIF
categories struct_biol and struct_biol_gen |
PDB,mmCIF |
|
ADDITIONAL
INFORMATION ABOUT EACH DEPOSITION:
|
Data Item |
Dictionary Item Name |
Status |
Comments |
|
Author
contact information |
mmCIF
category audit_contact_author |
PDB,mmCIF |
|
|
Release
status (e.g. release immediately, hold for 6 months) |
_pdbx_database_status.dep_release_code_coordinates _pdbx_database_status.dep_release_code_struct_fact _pdbx_database_status.dep_release_code_sequence |
PDB,mmCIF |
|
|
Citation |
mmCIF
categories citation and citation_author |
PDB,mmCIF |
|
|
Related
database information (e.g. sequence/target database ids) |
mmCIF
category pdbx_database_related |
PDB,mmCIF |
|
| ||
| © RCSB PDB | ||