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: