journal menudata 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
- 3. Model generation and refinement
- 4. Model validation
1. Sample information
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 |
| Rmerge 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 |
|
Rr.i.m. Rp.i.m. d-spacing (Å) at which < I/σ(I) > = 2 (if this does not occur, leave blank) dopt ![[info]](http://www.iucr.org/iucr-top/logos/info.gif){kind=small}
|
_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 Biso | _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 Biso | _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
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 Rwork | _refine.ls_R_factor_R_work _refine_ls_shell.R_factor_R_work |
| No. of reflections in test set for Rfree | _refine.ls_number_reflns_R_free _refine_ls_shell.number_reflns_R_free |
| Final Rfree | _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. |
|
