data for structural and crystallization communications

This page gives a list of recommended items for inclusion in structural and crystallization communications in Acta Crystallographica Section F.

The recommendations are tabulated below alongside the data names from the PDB mmCIF exchange dictionary available from the Protein Data Bank. These data items are provided in the mmCIF data sets created by the Protein Data Bank when a structure is deposited.

If you intend to submit to Acta Crystallographica Section F, you are recommended to use the PDB_EXTRACT utility available from the Protein Data Bank to extract as much as possible of this information from result and log files of most commonly-used macromolecular structure packages to create an initial mmCIF suitable for direct upload to the Protein Data Bank during the deposition process. A copy of the deposited mmCIF can then be uploaded to the journal to create standard tables for inclusion in your article.

The list below also includes examples to show how particular data will be organised in the mmCIF and how they will be arranged in the journal article.

Click here for a more compact summary of the recommendations.

1. Sample information
2. Data collection and structure solution statistics
- 2.1. Data collection, refinement data set
- 2.2. Phasing
3. Model generation and refinement
4. Model validation

1. Sample information
_symmetry.cell_setting
_symmetry.Int_Tables_number
_symmetry.space_group_name_H-M

Description	mmCIF items
1.1. Macromolecule and source information
Example 1: complex of E. coli glutamate decarboxylase α with glutarate Example 2: a zinc-induced heterodimer of two isoforms of phospholipase A₂ Example 3: mutation Example 4: mutation and modification
Structure name	_struct.title
Component molecules	_entity.pdbx_description
Additional molecular identifiers	ENTITY_NAME_SYS ENTITY_NAME_COM _entity.pdbx_ec
Biological functional unit (BFU) or macromolecular assembly, numbers and types of chains	_struct_biol.details
Mass of BFU (Da)	_struct_biol.pdbx_formula_weight _struct_biol.pdbx_formula_weight_method
Macromolecule sequence and chemical configuration
Sequence database reference code	_struct_ref.db_name _struct_ref.db_code
Polymers (one-letter code sequence)	_entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_seq_one_letter_code
or Polymer sequence as list of residues	_entity_poly_seq.num _entity_poly_seq.mon_id
Ligand, cofactor, ions, solvent	_pdbx_entity_nonpoly.name Small-molecule components will normally be identified as above by a pointer to an entry in the PDB ligand dictionary. Exceptionally, molecular details may be carried within the deposited mmCIF using data items from the appropriate categories: _chem_comp.id CHEM_COMP CHEM_COMP_ATOM CHEM_COMP_BOND
Mutations	_entity.pdbx_mutation
Post-translational modifications	_entity.pdbx_modification
Formula weight of entity (Da)	_entity.formula_weight or _entity.pdbx_formula_weight_exptl _entity.pdbx_formula_weight_exptl_meth
Source organism
Scientific name	_entity_src_nat.pdbx_organism_scientific
Strain	_entity_src_nat.strain
Details	_entity_src_nat.details
Source gene
Scientific name	_entity_src_gen.pdbx_gene_src_scientific_name
Strain	_entity_src_gen.gene_src_strain
Details	_entity_src_gen.gene_src_details
1.2 Macromolecule production
The link below illustrates how to supply information on sample preparation. Example: requested data for sample preparation.
For each macromolecular entity
PCR protocol	_pdbx_entity_prod_protocol.protocol _pdbx_entity_prod_protocol.protocol_type
Cloning protocol	_pdbx_entity_prod_protocol.protocol _pdbx_entity_prod_protocol.protocol_type
Expression protocol	_pdbx_entity_prod_protocol.protocol _pdbx_entity_prod_protocol.protocol_type
Purification protocol	_pdbx_entity_prod_protocol.protocol _pdbx_entity_prod_protocol.protocol_type
Additional details	_pdbx_entity_prod_protocol.protocol _pdbx_entity_prod_protocol.protocol_type
1.3. Crystallization
The links below illustrate several scenarios and should be consulted alongside the following list of items. Example 1: hanging-drop vapour diffusion Examples 2 and 3: different reservoir components Example 4: microbatch or liquid-liquid diffusion or dialysis method
Crystallization method	_exptl_crystal_grow.method _exptl_crystal_grow.method_ref
Temperature (K)	_exptl_crystal_grow.temp _exptl_crystal_grow.temp_details
Additional details Describe anything special about the method	_exptl_crystal_grow.details Examples: screens used and hits, optimization details, special conditions such as microgravity, magnetic field
Apparatus	_exptl_crystal_grow.apparatus
Atmosphere	_exptl_crystal_grow.atmosphere
Pressure (kPa)	_exptl_crystal_grow.pressure
Crystal growth time	_exptl_crystal_grow.time
Seeding	_exptl_crystal_grow.seeding _exptl_crystal_grow.seeding_ref
Volumes and pHs of crystallization solutions	_pdbx_exptl_crystal_grow_sol.volume _pdbx_exptl_crystal_grow_sol.volume_units _pdbx_exptl_crystal_grow_sol.pH
Compositions of crystallization solutions	_pdbx_exptl_crystal_grow_comp.comp_name _pdbx_exptl_crystal_grow_comp.conc _pdbx_exptl_crystal_grow_comp.conc_range _pdbx_exptl_crystal_grow_comp.conc_units
Cryo treatments
Final cryoprotection solution	_pdbx_exptl_crystal_cryo_treatment.final_solution_details
Soaking	_pdbx_exptl_crystal_cryo_treatment.soaking_details
Cooling	_pdbx_exptl_crystal_cryo_treatment.cooling_details
Annealing	_pdbx_exptl_crystal_cryo_treatment.annealing_details
1.4. Crystal data
Space group, crystal system
Unit-cell parameters (Å, °) (s.u. optional)	_cell.length_a _cell.length_a_esd _cell.length_b _cell.length_b_esd _cell.length_c _cell.length_c_esd _cell.angle_alpha _cell.angle_alpha_esd _cell.angle_beta _cell.angle_beta_esd _cell.angle_gamma _cell.angle_gamma_esd
Crystal dimensions or radius (mm)	_exptl_crystal.size_max _exptl_crystal.size_mid _exptl_crystal.size_min or _exptl_crystal.rad
Colour of crystal	_exptl_crystal.colour or _exptl_crystal.colour_primary _exptl_crystal.colour_modifier _exptl_crystal.colour_lustre
Crystal habit or shape	_exptl_crystal.description
No. of molecules in unit cell (Z)	_cell.formula_units_Z
Matthews coefficient V_M (Å³ Da^-1)	_exptl_crystal.density_Matthews
Solvent content (%)	_exptl_crystal.density_percent_sol

2. Data collection and structure solution statistics

Description	mmCIF items
2.1. Data collection, refinement data set
Example 1: data collection for a trypsin inhibitor and complexes of trypsin with the wild-type inhibitor and mutant, collected at different synchrotrons and with rotating-anode equipment.
Data set identifier	_database_2.database_id _database_2.database_code
Crystal sample conditions	exptl_crystal.preparation Examples: temperature, pressure, crystal mount, cryostat.
Diffraction protocol	_diffrn_radiation.pdbx_diffrn_protocol
Sampling protocol	_diffrn_measurement.device _diffrn_measurement.device_details _diffrn_measurement.method
Source of diffracting beam	_diffrn_source.source _diffrn_source.type
Focusing and collimation	_diffrn_radiation.collimation
Monochromator	_diffrn_radiation.monochromator
X-ray beam size	_diffrn_source.size
Wavelength (Å)	_diffrn_radiation.pdbx_wavelength _diffrn_radiation.pdbx_wavelength_list
Detector type	_diffrn_detector.detector _diffrn_detector.type
Temperature (K)	_diffrn.ambient_temp _diffrn.ambient_temp_esd _diffrn.ambient_temp_details
Total measuring time (s)	_diffrn_detector.pdbx_collection_time_total
No. of images	_diffrn_detector.pdbx_frames_total
Data-processing software	_computing.data_reduction This is the preferred data item for providing a succinct reference to the software package used for this purpose. Additional information about the package may also be provided using appropriate items in the category SOFTWARE
Resolution range (Å)	_reflns.d_resolution_low _reflns.d_resolution_high
and resolution range outer shell (Å)	_reflns_shell.d_res_low _reflns_shell.d_res_high
No. of unique reflections	_reflns.number_all _reflns.details _reflns_shell.number_unique_all
No. of observed reflections	_reflns.number_obs This item will only be used if a structure has not been refined, for example in reporting results of crystallization experiments. Otherwise, _refine.ls_number_reflns_obs will be reported under Section 3.
Criterion for observed reflections	_reflns.observed_criterion_sigma_F or _reflns.observed_criterion_sigma_I As above, these items will only be used if a structure has not been refined. Otherwise, the corresponding items for reflections used in the refinement will be reported under Section 3.
Completeness (%)	_reflns.percent_possible_obs _reflns_shell.percent_possible_obs
Redundancy	_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
< I/σ(I) > overall and by shell	_reflns.pdbx_netI_over_sigmaI _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs
R_merge overall and by shell	_reflns.Rmerge_F_all _reflns.Rmerge_F_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns.pdbx_Rmerge_I_all _reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs
R_r.i.m. R_p.i.m. d-spacing (Å) at which < I/σ(I) > = 2 (if this does not occur, leave blank) d_opt	_reflns.pdbx_Rrim_I_all _reflns.pdbx_Rpim_I_all _reflns.pdbx_res_netI_over_sigmaI_2 _reflns.pdbx_d_opt
2.2 Phasing
Phasing method	_phasing.method
2.2.1. MAD/SAD data and structure solution statistics
The link below illustrates characterization of data sets in MAD or related phasing methodologies. Example: MAD phasing of a stretch of double-stranded DNA bound to a drug molecule
MAD/SAD phasing method used	_phasing_MAD.method
Insertion of MAD/SAD scatterers	_phasing_MAD.details
Method of locating scatterers	_phasing_MAD.pdbx_anom_scat_method
No. of MAD/SAD sets used in phasing	_phasing_MAD.pdbx_number_data_sets
Phasing resolution range (Å)	_phasing_MAD.pdbx_d_res_low _phasing_MAD.pdbx_d_res_high
Phasing power all data; centric, acentric	_phasing_MAD.pdbx_power_centric _phasing_MAD.pdbx_power_acentric
Figure of merit overall	_phasing_MAD.pdbx_fom _phasing_MAD.pdbx_fom_centric _phasing_MAD.pdbx_fom_acentric
MAD/SAD solution software	_computing.structure_solution This is the preferred data item for providing a succinct reference to the software package used for this purpose. Additional information about the package may also be provided using appropriate items in the category SOFTWARE
For each phasing set
Radiation source	_phasing_set.radiation_source_specific
Radiation wavelength	_phasing_set.radiation_wavelength
Temperature (K)	_phasing_set.temp _phasing_set.pdbx_temp_details
Resolution range in the phasing data set (Å)	_pdbx_phasing_MAD_set.d_res_low _pdbx_phasing_MAD_set.d_res_high
f' used in phasing	_phasing_MAD_set.f_prime
f'' used in phasing	_phasing_MAD_set.f_double_prime
Phasing power by set; centric, acentric	_pdbx_phasing_MAD_set.power_centric _pdbx_phasing_MAD_set.power_acentric
No. of sites	_pdbx_phasing_MAD_set.number_of_sites
For each of the sites, the following: site no., atom symbol, occupancy, x, y, z and B_iso	_pdbx_phasing_MAD_set_site.id _pdbx_phasing_MAD_set_site.atom_type_symbol _pdbx_phasing_MAD_set_site.occupancy _pdbx_phasing_MAD_set_site.fract_x _pdbx_phasing_MAD_set_site.fract_y _pdbx_phasing_MAD_set_site.fract_z _pdbx_phasing_MAD_set_site.B_iso
2.2.2. MIR/MIRAS/SIR/SIRAS data and structure solution statistics
The link below illustrates characterization of data sets in MIR or related phasing methodologies, in the cases where the native data set is and is not used for refinement. Example: use of a samarium derivative and the SIRAS method
For the MIR application as a whole:
No. of derivatives	_phasing_MIR.pdbx_number_derivatives
Description of the phasing strategy	_phasing_MIR.details
Resolution range of phasing (Å)	_phasing_MIR.d_res_low _phasing_MIR.d_res_high
Phasing power all data; acentric, centric	_phasing_MIR_der.power_acentric, _phasing_MIR_der.power_centric
Figure of merit all data	_phasing_MIR.FOM _phasing_MIR.FOM_centric _phasing_MIR.FOM_acentric
MIR solution software	_computing.structure_solution This is the preferred data item for providing a succinct reference to the software package used for this purpose. Additional information about the package may also be provided using appropriate items in the category SOFTWARE
For each phasing data set (if the native data set used for phasing is not the set used for refinement, it should be described as the first phasing set; additional data sets will correspond to each of the derivatives):
Radiation source	_phasing_set.radiation_source_specific
Radiation wavelength	_phasing_set.radiation_wavelength
Temperature (K)	_phasing_set.temp _phasing_set.pdbx_temp_details
Resolution range of phasing data set (Å)	_phasing_set.pdbx_d_res_low _phasing_set.pdbx_d_res_high
Then, for each derivative:
Derivative	_phasing_MIR_der.id
Derivative preparation	_phasing_MIR_der.details
Heavy-atom location method	_phasing_MIR.method
Number of sites	_phasing_MIR_der.number_of_sites
Figure of merit	_phasing_MIR_der.pdbx_fom _phasing_MIR_der.pdbx_fom_centric _phasing_MIR_der.pdbx_fom_acentric
For each of the sites, the following: site no., atom symbol, occupancy, x, y, z and B_iso	_phasing_MIR_der_site.id _phasing_MIR_der_site.atom_type_symbol _phasing_MIR_der_site.occupancy _phasing_MIR_der_site.fract_x _phasing_MIR_der_site.fract_y _phasing_MIR_der_site.fract_z _phasing_MIR_der_site.B_iso
2.2.3. Molecular replacement data and structure solution statistics
The link below illustrates characterization of data sets in molecular replacement phasing methodologies, in the cases where the native data set is and is not used for refinement. Example: phasing of a DNA octamer using the molecular replacement method
PDB code for search model	_pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type
or Identification of search model	_refine.pdbx_starting_model
If phasing data set is not the data set used for refinement:
Radiation source	_phasing_set.radiation_source_specific
Radiation wavelength (Å)	_phasing_set.radiation_wavelength
Temperature (K)	_phasing_set.temp _phasing_set.pdbx_temp_details
Resolution range (Å)	_phasing_set.pdbx_d_res_low _phasing_set.pdbx_d_res_high
Molecular replacement phasing details
Alterations to the search model	_pdbx_phasing_MR.model_details
MR solution software	_computing.structure_solution This is the preferred data item for providing a succinct reference to the software package used for this purpose. Additional information about the package may also be provided using appropriate items in the category SOFTWARE

3. Model generation and refinement

Description	mmCIF items
Example 1: a 2'-5' RNA ligase Example 2: M. tuberculosis pyR protein
Structure refinement software	_computing.structure_refinement This is the preferred data item for providing a succinct reference to the software package used for this purpose. Additional information about the package may also be provided using appropriate items in the category SOFTWARE
Refinement on \|F\|, I, or F²	_refine.ls_structure_factor_coef
σ cutoff in data	(one of) _refine.pdbx_ls_sigma_F _refine.pdbx_ls_sigma_I _refine.pdbx_ls_sigma_Fsqd
Resolution range (Å)	_refine.ls_d_res_low _refine.ls_d_res_high
and resolution range outer shell (Å)	_refine_ls_shell.d_res_low _refine_ls_shell.d_res_high
No. of reflections used in refinement	_refine.ls_number_reflns_R_work _refine_ls_shell.number_reflns_R_work
No. of reflections above σ cutoff in final cycle	_refine.ls_number_reflns_obs _refine_ls_shell.number_reflns_obs
Final overall R factor	_refine.ls_R_factor_obs _refine_ls_shell.R_factor_obs
Atomic displacement model (iso, aniso, mixed)	_refine_B_iso.treatment _refine_B_iso.class
Overall average B factor excluding solvent (Å²)	_refine.B_iso_mean _refine.B_iso_min _refine.B_iso_max
No. of macromolecule atoms refined	_refine_hist.pdbx_number_atoms_protein _refine_hist.pdbx_number_atoms_nucleic_acid
No. of ligand atoms	_refine_hist.pdbx_number_atoms_ligand
No. of solvent atoms	_refine_hist.number_atoms_solvent
Total No. of atoms	_refine_hist.number_atoms_total
No. of refined parameters	_refine.ls_number_parameters
Non-crystallographic symmetry restraints	_refine_ls_restr_ncs.ncs_model_details
Bulk solvent model	_refine.solvent_model_param_bsol _refine.solvent_model_param_ksol _refine.solvent_model_details

4. Model validation

Description	mmCIF items
The examples are those used also in Section 3 above: Example 1: a 2'-5' RNA ligase Example 2: M. tuberculosis pyR protein
Final R_work	_refine.ls_R_factor_R_work _refine_ls_shell.R_factor_R_work
No. of reflections in test set for R_free	_refine.ls_number_reflns_R_free _refine_ls_shell.number_reflns_R_free
Final R_free	_refine.ls_R_factor_R_free _refine_ls_shell.R_factor_R_free
Cruickshank DPI	_refine.overall_SU_R_Cruickshank_DPI
R.m.s. deviations from target values for bond distances, bond angles and isotropic B factors (overall, main chain and side chain)	_refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number
Ramachandran plot analysis most favoured regions (%) additionally allowed regions (%) generously allowed regions (%) disallowed regions (%)	PDBX_FEATURE_SEQUENCE_RANGE
The links below illustrate the presentation of Ramachandran plot summary metrics for a single complete protein molecule, and for different sequence ranges within a more complex structure. Example 1: Ramachandran plot statistics for a single complete protein molecule Example 2: Ramachandran plot statistics for the two chains of a heterodimer
Omitted residues	PDBX_FEATURE_MONOMER
The link below illustrates how to account for missing and partial residues in the refined model. Example: missing and partial residues.