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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: