data for structural and crystallization communications

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

The primary purpose of this page is to solicit the opinions and suggestions of members of the Acta D and F Editorial Boards on what information should be required of authors in articles describing macromolecular structures. The page is modelled on the list of requested items published by the journal. An expanded page with details of the individual mmCIF data items is also available and board members are urged to consult it frequently. This latter page often provides a deeper, richer description of what is requested than is possible on this page. It is also liberally decorated with crystallographically realistic examples that are (1) rendered in full-blown mmCIF and (2) also shown in the proposed tabular form that the Editorial Office will convert the mmCIF into upon receipt. We urge you to look at these pages and welcome your comments and suggestions on them in addition to those related to data required for publication. A caution: the two lists, the one on this page and the one with details of the individual mmCIF data items, while beginning with a one-to-one correspondence in data descriptors and in data order, have despite our best efforts, drifted away from that correspondence a bit here and there. It is our intention to repair that drift soon, but we would rather not further delay soliciting your opinions and suggestions.

In the listings below, to initiate the discussion, we have rendered some items in a red typeface. We offer these as principal candidates for data that should be considered mandatory; that is, these data or their equivalents should be presented in the article either (1) within the standard experimental tables that will be auto-generated from the author's deposited mmCIF (in most cases this is the preferred location) or (2) within the main text of the article.

Note that standards we have discussed and adopted, two so far, are accessible via buttons placed at relevant locations. An enzyme-naming convention is also included. Please use this exercise to suggest areas where additional consensus standards may be needed. One we've considered is a standard for unbiased indication of resolution and I hope we can achieve consensus on this concern quickly. I also note the popularity of giving average values of atomic displacement parameters, overall, main chain and side chain, in lieu of r.m.s.d.s from target values.

Once we have a reasonable consensus of the required data, it is our understanding that a version of the RCSB deposition GUI will be made available that will prompt depositors who identify themselves as would-be authors for the required data at time of deposition. Happily, much of the data we propose be designated as required can be taken automatically from the depositors log and output files if they employ the PDB_EXTRACT tool RCSB provides. The mmCIF file created at deposition can then be provided to the Editorial Office at submission time for conversion to tabular form. Our list of requirements will present a significant challenge for authors who want to prepare a fully compliant mmCIF file for transfer to the journal. Authors are not required to provide all required data in mmCIF format; they may supply missing data in text or additional tables at submission time if they choose. Success of collecting this level of detail at time of deposition will depend heavily on (1) cooperation of software developers to output the desired information in a dictionary compliant manner, and (2) authors taking advantage of tools like PDB_EXTRACT to automatically harvest this information from their program output files.

For now, it is envisaged that, as an aid to editors, the review document produced by the online submission system will indicate which of the required data are absent from the mmCIF. Where they are absent from the mmCIF (and thus from the standard experimental table), reviewers should ensure that they are discussed within the appropriate experimental section of the article text.

As an aside, if you explore the other pages, you will see that there are a number of mmCIF items ("*.details" items) that accept text instead of specific data. Some of these appear unavoidable, but we are open to suggestions for improvement. The use of text items reaches its nadir in Section 1.2 on protein preparation. RCSB has prepared an expansion of the mmCIF for preparation that appears complete and is a rich trove of items we could use, but we are advised that at present the relevant community is largely unwilling to deposit using these items. RCSB will not be able to do any translation of information in "*.details" items into specific data items, and at the journal these data will simply be tabulated or, if of significant length, placed in supplementary material. It is our fondest hope that in the near future, as automation and LIMS advance further into everyday use, we will be able to replace the current Section 1.2 with one that accepts specific data in specific mmCIF items. We realize, too, that we must be ever vigilant for changing practices that require changes in our use of mmCIF and in our required data, for change they will, of that we can be certain.

With regard to imposition of data requirements on submitting authors, it is understood that editors are to exercise common sense and appropriate judgement in cases where required data should in fact be omitted (for example, because they do not make sense in the context of a particular design of experiment).

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1. Sample information

1.1. Macromolecule and source information

Molecular definition

Structure name

Component molecules

Additional molecular identifiers

Biological functional unit (BFU) or          macromolecular assembly, numbers and types of chains

Mass of BFU (Da)

Macromolecule sequence and chemical configuration

Sequence database reference code

Polymers (one-letter code sequence) or Polymer sequence as list of residues

Ligand, cofactor, ions, solvent

Mutations

Post-translational modifications

Formula weight of entity (Da)

Source organism

Scientific name

Strain

Details

Source gene

Scientific name

Strain

Details

1.2 Macromolecule production

For each macromolecular entity

PCR protocol (required if recombinant, otherwise absent)

Cloning protocol (required if recombinant, otherwise absent)

Expression protocol (required if recombinant, otherwise absent)

Purification protocol

Additional details

1.3. Crystallization

Crystallization specifics

Crystallization method

Temperature (K)

Additional details

Apparatus

Atmosphere

Pressure (kPa)

Crystal growth time

Seeding

Volumes and pHs of crystallization solutions

Compositions of crystallization solutions

Cryo treatments

Final cryoprotection solution

Soaking

Cooling

Annealing

1.4. Crystal data

Space group, crystal system

Unit-cell parameters (Å, °) (s.u. optional)

Crystal dimensions or radius (mm)

Colour of crystal

Crystal habit or shape

No. of molecules in unit cell (Z)

Matthews coefficient VM (Å3 Da-1)

Solvent content (%)

2. Data collection and structure solution statistics

2.1. Data collection, refinement data set

Data set identifier

Crystal sample conditions

Diffraction protocol

Sampling protocol

Source of diffracting beam

Focusing and collimation

Monochromator

X-ray beam size

Wavelength (Å)

Detector type

Temperature (K)

Total measuring time (s)

No. of images

Data-processing software

Resolution range (Å) (overall and outer shell)

No. of unique reflections (overall and outer shell)

No. of observed reflections (only for unrefined structures, e.g. crystallization experiments)

Criterion for observed reflections (only for unrefined structures, e.g. crystallization experiments)

Completeness (%) (overall and outer shell)

Redundancy (overall and outer shell)

< I/σ(I) > (overall and outer shell)

Rmerge (overall and outer shell)

Rr.i.m.      Rp.i.m.      d-spacing (Å) at which < I/σ(I) > = 2 (if this does not occur, leave blank)      dopt

2.2 Phasing

Phasing method

2.2.1. MAD/SAD data and structure solution statistics

For the MAD/SAD application as a whole:

MAD/SAD phasing method used

Insertion of MAD/SAD scatterers

Method of locating scatterers

No. of MAD/SAD sets used in phasing

Phasing resolution range (Å)

Phasing power all data; centric, acentric

Figure of merit overall

MAD/SAD solution software

For each phasing set

Radiation source

Radiation wavelength

Temperature (K)

Resolution range in the phasing data set (Å)

f' used in phasing

f'' used in phasing

Phasing power by set; centric, acentric

And again for the MAD/SAD application as a whole:

No. of sites

For each of the sites, the following: site no., atom symbol, occupancy, x, y, z and Biso

2.2.2. MIR/MIRAS/SIR/SIRAS data and structure solution statistics

For the MIR application as a whole:

No. of derivatives

Description of the phasing strategy

Resolution range of phasing (Å)

Phasing power all data; acentric, centric

Figure of merit all data

MIR solution 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

Radiation wavelength

Temperature (K)

Resolution range of phasing data set (Å)

Then, for each derivative:

Derivative

Derivative preparation

Heavy-atom location method

Number of sites

Figure of merit

For each of the sites, the following: site no., atom symbol, occupancy, x, y, z and Biso

2.2.3. Molecular replacement data and structure solution statistics

Search model

PDB code for search model

or Identification of search model

If phasing data set is not the data set used for refinement:

Radiation source

Radiation wavelength (Å)

Temperature (K)

Resolution range (Å)

Molecular replacement phasing details

Alterations to the search model

MR solution software

3. Model generation and refinement

    

Structure refinement software

Refinement on |F|, I, or F2

σ cutoff in data

Resolution range (Å) (overall and outer shell)

No. of reflections used in refinement (overall and outer shell)

No. of reflections above σ cutoff in final cycle (overall and outer shell)

Final overall R factor (overall and outer shell)

Atomic displacement model (iso, aniso, mixed)

Overall average B factor for the macromolecule(s) excluding solvent (Å2)

No. of macromolecule atoms refined

No. of ligand atoms

No. of solvent atoms

Total No. of atoms

No. of refined parameters

Non-crystallographic symmetry restraints

Bulk solvent model

4. Model validation

Final Rwork (overall and outer shell)

No. of reflections in test set for Rfree (overall and outer shell)

Final Rfree (overall and outer shell)

Cruickshank DPI

R.m.s. deviations from target values for bond distances, bond angles and       isotropic B factors (overall, main chain and side chain)

Ramachandran plot analysis          most favoured regions (%)          additionally allowed regions (%)          generously allowed regions (%)          disallowed regions (%)

Omitted residues