journal menudata for structural communications
This page gives a list of recommended items for publication in structural communications in Acta Crystallographica Section F.
In the tables below, data names in gray are proposed items in the PDBX exchange dictionary that have not yet been implemented; data names in red are suggested corrections to names or additional names required in the PDBX exchange dictionary.
1. Sample information
| Description | mmCIF items |
| 1.1. Macromolecule and source information | |
| Structure name | _struct.title |
| Component molecules | _entity.pdbx_description |
| Biological functional unit or macromolecular assembly, numbers and types of chains | _struct_biol.details |
| Macromolecule sequence and chemical configuration | |
| 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 |
| Ligands, cofactors, ions, solvent |
_pdbx_entity_nonpoly.name _chem_comp.id CHEM_COMP CHEM_COMP_ATOM CHEM_COMP_BOND |
| Sequence database code | _struct_ref.db_name _struct_ref.db_code |
| Mutations | _entity.pdbx_mutation |
| Post-translational modifications | _entity.pdbx_modification |
| Macromolecule weight (Da) | _struct.pdbx_asym_formula_wt_derived |
| Source organism | |
| Scientific name | _entity_src_nat.pdbx_organism_scientific |
| Strain | _entity_src_nat.strain |
| Additional details | _entity_src_nat.details |
| Source gene | |
| Scientific name | _entity_src_gen.pdbx_gene_src_scientific_name |
| Organ | _entity_src_gen.pdbx_gene_src_organ |
| American Type Culture Collection No. | _entity_src_gen.pdbx_gene_src_atcc |
| Cellular location | _entity_src_gen.pdbx_gene_src_cellular_location (OK?) |
| Expression system | |
| Scientific name | _entity_src_gen.pdbx_host_org_scientific_name |
| Cell line | _entity_src_gen.pdbx_host_org_cell_line |
| Strain | _entity_src_gen.pdbx_host_org_strain |
| Variant | _entity_src_gen.pdbx_host_org_variant |
| Additional details | _entity_src_gen.host_org_details |
| Host expression vector, plasmid | |
| Vector | _entity_src_gen.pdbx_host_org_vector |
| Plasmid | _entity_src_gen.plasmid_name |
| Additional details | _entity_src_gen.plasmid_details |
| 1.2 Macromolecule production | |
|
At deposition, data related to preparation of sample will be accepted
by RCSB in free-text form. This section of the data can be
transmitted to the journal along with the mmCIF file for the other
sections of the data and included in the manuscript as is, apart from
some changes in type and format. This section will, of course, also
be governed by the requirements for some data for publication and to
help author/depositors in meeting those requirements at time of
deposition, lists of topics requiring explicit data are provided.
These lists are outlines of the important experimental steps that need
to be described. The text that presents these data should necessarily
be brief and may be in a style of the author's choosing, but the
content should be sufficient to meet the classical requirement for
publication, that is, that it permit a reader unambiguously to
replicate the experiments with sufficient fidelity to be successful in
achieving the published result.
In constructing the free-text description of a sample preparation from a naturally occurring source, the depositor should include specifics on the following: 1) Extraction, including as needed mechanical steps, use of solvents, delipidation and other treatments. 2) Fractionation, including details of centrifugation, differential precipitation and resolution, chromatographic steps (volumes, concentrations, buffers, flow rates, elution protocols, temperatures), pooling of fractions and resultant volumes, estimates of yield. 3) Other steps as needed, including, proteolytic treatments and refolding steps. 4) Purification, including dialysis and transfer to storage buffer, composition of storage buffer, final concentration steps, protein characterization, estimate of purity, yield and method of estimation, storage temperature. For protein production from modern artificial sources, the extraction segment should be replaced by the following: 1) Preparation of vector, including restriction enzymes digestions as needed; explicit description of the region of protein expressed with numbering referenced to a specific entry in a publicly available sequence database (e.g. NCBI RefSeq, GenBank, Swiss-Prot, etc); PCR steps; cloning steps including methods, conditions, and details of ligation or recombination; method of transformation; modifications of vector; purification of cloned product; marker for transformed cells. 2) Expression, including promoter; tagging procedures and sequences; volume and contents of media; incubation; details of induction, transformation or transfection; harvesting and storage of culture. 3) Lysis, including method, composition and volume of buffer, time, temperature, and other details as necessary. To this should be added the final three segments listed above for natural products (as segments 4, 5, and 6), with special attention being paid to explicitly specifying the retention or removal of any tags and any refolding treatments that are used. If ligand must be introduced at any step during the preparation, this process should be explicitly described. | |
| For each macromolecular entity | |
| Target selection protocol | _entity_pdbx_prod_protocol.target_selection |
| PCR protocol | _entity_pdbx_prod_protocol.pcr |
| Cloning protocol | _entity_pdbx_prod_protocol.cloning |
| Expression protocol | _entity_pdbx_prod_protocol.expression |
| Purification protocol | _entity_pdbx_prod_protocol.purification |
| Additional details | _entity_pdbx_prod_protocol.details |
| 1.3. Crystallization | |
| Crystallization method | _exptl_crystal_grow.method _exptl_crystal_grow.method_ref |
| Temperature (K) |
_exptl_crystal_grow.temp _exptl_crystal_grow.temp_details |
| Special conditions (eg microgravity, magnetic field, pressure) | _exptl_crystal_grow.details |
| Solution composition (identifiers) |
_pdbx_exptl_crystal_grow_sol.crystal_id _pdbx_exptl_crystal_grow_sol.sol_id _pdbx_exptl_crystal_grow_comp.crystal_id _pdbx_exptl_crystal_grow_comp.sol_id _pdbx_exptl_crystal_grow_comp.comp_id |
| 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 |
_symmetry.cell_setting _symmetry.Int_Tables_number _symmetry.space_group_name_H-M |
| 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 size (mm) | _exptl_crystal.size_max _exptl_crystal.size_mid _exptl_crystal.size_min |
| Colour of crystal | _exptl_crystal.colour |
| Crystal shape | _exptl_crystal.description |
| No. of molecules in unit cell (Z) | _cell.formula_units_Z |
| Matthews coefficient VM (Å3 Da-1) | _exptl_crystal.density_Matthews |
| Solvent content (%) | _exptl_crystal.density_percent_sol |
