Notes for authors 2003

1. Scientific scope

Section D of Acta Crystallographica welcomes the submission of papers covering any aspect of structural biology, particularly structures of biological macromolecules. In addition to new structural determinations, preliminary data on unit-cell dimensions and space groups will be considered for publication, provided suitable diffraction photographs (or their equivalent), together with an estimate of resolution, are included. Also, articles on crystal growth of biological macromolecules are welcomed, and refinements of known structures may be published if the information content warrants it. For all structural papers, sufficient evidence should be provided to convince the referees that the interpretations of the diffraction data and electron-density maps are correct, within the resolution of the analysis.

2. Categories of contributions

Contributions should conform to the general editorial style of the journal.

2.1. Research Papers

Full-length Research Papers should not normally exceed 15 journal pages (about 15 000 words).

2.2. Short Communications

Short Communications are intended for the presentation of topics of limited scope, or for preliminary announcements of novel research findings. They are not intended for interim reports of work in progress, and must report results that are of scientific value in their own right.

Short Communications should not exceed two journal pages (about 1500 words). A maximum of two figures and two tables of appropriate size are permitted.

2.3. Crystallization Papers

These are short papers which report the crystallization of novel, important or difficult-to-crystallize biological macromolecules, or new crystallization techniques. In general, a submission will only be considered if the structure of the macromolecule has not been published already.

Crystallization Papers should not normally exceed two journal pages (about 1500 words). Authors should take into account the evaluation criteria given in §11.

Crystallization Papers should be submitted to one of the Crystallization Co-editors, whose addresses appear on the inside front cover of each issue.

2.12. Structural Genomics Papers

This category of papers provides rapid reporting of structural genomics research. Full details can be found at //journals.iucr.org/d/services/structuralgenomics/ .

2.4. Lead Articles

Lead Articles are authoritative, comprehensive and forward-looking reviews of major areas of research interest. They are always commissioned by the Section Editors, on the advice of the Editorial Board. Suggestions for suitable topics and of potential author(s) are welcomed by the Section Editors for discussion with the Board.

The Section Editors will discuss the treatment of the topic, the length of the Article and the delivery date of the manuscript with invited author(s); Lead Articles will be refereed in the normal manner.

2.5. Topical Reviews

A Topical Review is a short, highly focused survey covering a relatively narrow area of current research interest. It should not aim to be comprehensive, but a brief introduction should provide historical perspective and a brief conclusion should indicate likely future directions.

Topical Reviews will be limited to about ten journal pages (10 000 words) except in special agreed circumstances. Shorter reviews on rapidly evolving areas are also actively encouraged. They will be commissioned by the Section Editors either personally, or following a formal proposal by prospective author(s). Topical Reviews will be refereed in the normal way.

2.6. Letters to the Editor

These may deal with non-technical aspects of crystallography, its role, its propagation, the proper function of its Societies etc., or may make a technical observation that would usefully be brought to a wider audience. Letters should be submitted to one of the Section Editors or to the Editor-in-chief of Acta Crystallographica only.

2.7. Scientific Comment

Comments of general scientific interest to the readership are welcomed. These should not normally exceed two journal pages and should be submitted as in §3.

2.8. Meeting Reports

These are normally invited. Prospective authors interested in writing such items should first contact the Section Editors.

2.9. New Commercial Products

Announcements of new commercial products are published free of charge. The descriptions, up to 300 words or the equivalent if a figure is included, should give the manufacturer's full address.

2.10. Obituaries

These will be commissioned by the Section Editors.

3. Submission and handling of manuscripts

Papers should be submitted in one of two ways: as hard copy directly to a Co-editor or Section Editor or electronically via the web at //journals.iucr.org/services/submit.html .

3.1. Hard-copy submission

Manuscripts and figures should be prepared using the file formats listed in §3.9. Three paper copies and the electronic file(s) should be submitted; authors are reminded to keep an exact copy of the submission for later editorial adjustments and for checking proofs. Unless stated otherwise in §2, the submission should be sent to a Section Editor or any of the Co-editors taking into account their areas of expertise. On acceptance, an electronic version of the final manuscript will be required by the Editorial Office.

Contact details for the editors are available at //journals.iucr.org/d/services/editors.html .

3.2. Electronic submission

Manuscripts and figures should be prepared using the file formats listed in §3.9. Full details of the submission procedure can be found at //journals.iucr.org/services/submit.html and authors should first check this page to see if the service is available.

3.3. Languages of publication

Acta Crystallographica Section D will publish papers in English, French, German and Russian.

3.4. Handling of manuscripts

All contributions will be seen by referees (normally two) before they can be accepted for publication. The editor to whom the manuscript is assigned is responsible for choosing referees and for accepting or rejecting the paper. This responsibility includes decisions on the final form of the paper and interpretation of these Notes when necessary.

If changes to a manuscript requested by a Section Editor, Co-editor or the editorial staff are not received within two months of transmittal to the author, the submission will automatically be withdrawn. Should the manuscript require further revision, this would normally be expected to be completed within one month of the revision having been requested. Any subsequent communication of the material will be treated as a new submission in the editorial process.

For accepted papers, it is the responsibility of the Managing Editor to prepare the paper for printing. This may involve correspondence with the authors and/or the responsible editor in order to resolve ambiguities or to obtain satisfactory figures or tables. The date of acceptance that will appear on the published paper is the date on which the Managing Editor receives the last item required. Correspondence will be sent to the author who submitted the paper unless the Managing Editor is informed of some other suitable arrangement.

On rare occasions an editor may consider that a paper is better suited to a section of Acta Crystallographica other than that specified by the author(s), to the Journal of Applied Crystallography or to the Journal of Synchrotron Radiation. Any change to the section or journal of publication will only be made after full discussion with the communicating author.

3.5. Author's warranty

The submission of a paper is taken as an implicit guarantee that the work is original, that it is the author(s) own work, that all authors concur with and are aware of the submission, that all workers involved in the study are listed as authors or given proper credit in the acknowledgements, that the manuscript has not already been published (in any language or medium), and that it is not being considered and will not be offered elsewhere while under consideration for an IUCr journal. The inclusion of material in an informal publication, e.g. a preprint server or a newsletter, does not preclude publication in an IUCr journal. All authors will be required to sign off the final version of the paper.

Important considerations related to publication have been given in the ethical guidelines published in Acc. Chem. Res. (2002), 35, 74–76.

3.6. Copyright

Except as required otherwise by national laws, an author must sign and submit a copy of the Transfer of Copyright Agreement form for each manuscript before it can be accepted. During the electronic submission process, authors will be asked to transfer copyright electronically.

3.7. Author grievance procedure

An author who believes that a paper has been unjustifiably treated by the Co-editor may appeal initially to a Section Editor and then to the Editor-in-chief if still aggrieved by the decision.

3.8. Contact e-mail address

The contact author must provide an e-mail address for editorial communications and despatch of electronic proofs.

3.9. File format

The manuscript should be prepared using T_EX, L^AT_EX or Word. Authors are encouraged to use the templates available from the Editorial Office by e-mail ([e-mail]) or by ftp (from the `templates' directory). All Word submissions should be accompanied by an RTF (rich text format) file.

Figures may be provided in PostScript, encapsulated PostScript or TIFF formats. The resolution of bitmap graphics should be a minimum of 600 d.p.i.

3.10. File transfer

For electronic submissions the files should be uploaded via the web. Full details of this procedure are given at //journals.iucr.org/services/submit.html .

For hard-copy submissions final electronic files must have a filename constructed from the reference number supplied by the Co-editor. Files should be given the extensions .tex, .doc and .rtf as appropriate. Illustrations should be given the extensions .ps, .eps or .tif. Multiple files for the same submission should be uniquely identified e.g. xz1087fig1.ps, xz1087fig2.ps, xz1087.doc, etc. where xz1087 is the reference number.

Only after acceptance of the paper by the responsible editor should the final electronic version of the paper be sent to the Editorial Office in Chester. This may be via the web (see above), by e-mail ([e-mail]), on diskette or by ftp as described below.

Table 1

(i) On your workstation enter:	ftp ftp.iucr.org
(ii) Wait for Name…: prompt and enter:	anonymous
(iii) Wait for Password: prompt and enter:	your e-mail address
(iv) Wait for ftp> prompt and enter:	cd incoming/d
(v) Transfer a file from your account (e.g. j29.ps) as an identifiable name (e.g.xz1087fig1.ps):	put j29.ps xz1087fig1.ps
(vi) Wait for ftp> prompt before sending another file
(vii) Finish off the ftp session by entering:	bye
(viii) Send an e-mail to Chester ([e-mail]) with a list of the files transferred by ftp

4. Abstract and synopsis

All contributions must be accompanied by an English language Abstract and a one or two sentence Synopsis of the main findings of the paper for inclusion in the Table of Contents for the relevant issue. The Abstract should state as specifically and as quantitatively as possible the principal results obtained.

The Abstract should be suitable for reproduction by abstracting services without change in wording. It should not repeat information given in the title. Ordinarily 200 words suffice for Abstracts of Research Papers, Lead Articles and Topical Reviews, and 100 words for shorter contributions. It should make no reference to tables, diagrams, atom numbers or formulae contained in the paper. It should not contain footnotes. Numerical information given in the Abstract should not be repeated in the text. It should not include the use of `we' or `I'.

Literature references in an Abstract are discouraged. If a reference is unavoidable, it should be sufficiently full within the Abstract for unambiguous identification, e.g. [Terwilliger (1994). Acta Cryst. D50, 17–23].

5. Diagrams and photographs (`figures')

Figures should be prepared using one of the file formats listed in §3.9.

The choice of tables and figures should be optimized to produce the shortest printed paper consistent with clarity. Duplicate presentation of the same information in both tables and figures is to be avoided, as is redundancy with the text.

Authors of protein structure papers are requested to submit a picture of the Cα chain trace. This will be helpful for referees and may be deposited. In addition, a diagram of the fit of a side chain is helpful to the reader in terms of assessing the resolution and map quality.

Fibre data should contain appropriate information such as a photograph of the data. As primary diffraction data cannot be satisfactorily extracted from such figures, the basic digital diffraction data should be deposited.

5.1. Quality

Electronic files in the formats listed in §3.9 are essential for high-quality reproduction. The resolution of bitmap graphics should be a minimum of 600 d.p.i. Where electronic files are not available, hard-copy greyscale or colour images should be provided as glossy prints. Laser printer or photocopier output will generally be unsatisfactory for reproduction of such diagrams.

5.2. Size

Diagrams should be as small as possible consistent with legibility. They will normally be sized so that the greatest width including lettering is less than the width of a column in the journal.

5.3. Lettering and symbols

Fine-scale details and lettering must be large enough to be clearly legible (ideally 1.5–3 mm in height) after the whole diagram has been reduced to one column width.

Lettering should be kept to a minimum; descriptive matter should be placed in the legend.

5.4. Numbering and legends

Diagrams should be numbered in a single series in the order in which they are referred to in the text. A list of the legends (`figure captions') should be included in the manuscript.

5.5. Stereofigures

Atom labelling when included should be on both left and right views in stereo perspective. Both views should be incorp­orated into a single figure.

5.6. Colour figures

Figures in colour are accepted at no cost to the author provided that the editor agrees that they improve the understanding of the paper. At the editor's discretion, figures printed in black and white may appear in colour in Crystallography Journals Online.

6. Tables

Authors submitting in Word should use the Word table editor to prepare tables.

6.1. Use of tables

Extensive numerical information is generally most economically presented in tables. Text and diagrams should not be redundant with the tables.

6.2. Design, numbering and size

Tables should be numbered in a single series of arabic numerals in the order in which they are referred to in the text. They should be provided with a caption.

Tables should be carefully designed to occupy a minimum of space consistent with clarity.

7. Mathematics and letter symbols

Authors submitting in Word should use the Word equation editor to prepare displayed mathematical equations.

The use of the stop (period) to denote multiplication should be avoided except in scalar products. Generally no sign is required but, when one is, a multiplication sign (×) should be used.

Vectors should be in bold type and tensors should be in bold-italic type.

Greek letters should not be spelled out.

Care should be taken not to cause confusion by using the same letter symbol in two different meanings.

Gothic, script or other unusual lettering should be avoided. Another typeface may be substituted if that used by the author is not readily available.

Equations, including those in published Appendices, should be numbered in a single series.

8. Multimedia

Multimedia additions to a paper (e.g. time-lapse sequences, three-dimensional structures) are welcomed; they will be made available via Crystallography Journals Online.

9. Nomenclature

9.1. Crystallographic nomenclature

Authors should follow the general recommendations produced by the IUCr Commision on Crystallographic Nomenclature (see reports at https://www.iucr.org/iucr-top/comm/cnom/ ).

Atoms of the same chemical species within an asymmetric unit should be distinguished by an appended arabic numeral. Chemical and crystallographic numbering should be in agreement wherever possible. When it is necessary to distinguish crystallographically equivalent atoms in different asymmetric units the distinction should be made by lower-case roman numeral superscripts (i.e. i, ii, iii etc.) to the original atom labels.

Space groups should be designated by the Hermann–Mauguin symbols. Standard cell settings, as listed in Volume A of International Tables for Crystallography, should be used unless objective reasons to the contrary are stated. When a non-standard setting is used, the list of equivalent positions should be given. Hermann–Mauguin symbols should also be used for designating point groups and molecular symmetry. It is helpful if the origin used is stated explicitly where there is a choice.

The choice of axes should normally follow the recommendations of the Commission on Crystallographic Data [Kennard et al. (1967). Acta Cryst. 22, 445–449 ].

A symbol such as 123 or hkl without brackets is understood to be a reflection, (123) or (hkl) a plane or set of planes, [123] or [uvw] a direction, {hkl} a form and 〈uvw〉 all crystallographically equivalent directions of the type [uvw]. Other bracket notations should be explicitly defined.

9.2. Nomenclature of chemical compounds etc.

Chemical formulae and nomenclature should conform to the rules of nomenclature established by the International Union of Pure and Applied Chemistry (IUPAC ), the International Union of Biochemistry and Molecular Biology (IUBMB ), the International Mineralogical Association and other appropriate bodies. As far as possible the crystallographic nomenclature should correspond to the systematic name.

Any accepted trivial or non-systematic name may be retained, but the corresponding systematic (IUPAC) name should also be given.

9.3. Units

The International System of Units (SI ) is used except that the ångström (symbol Å, defined as 10⁻¹⁰ m) is generally preferred to the nanometre (nm) or picometre (pm) as the appropriate unit of length. Recommended prefixes of decimal multiples should be used rather than `× 10ⁿ'.

10. References

References to published work must be indicated by giving the authors' names followed immediately by the year of publication, e.g. Neder & Schulz (1998) or (Neder & Schulz, 1998). Where there are three or more authors the reference in the text should be indicated in the form Smith et al. (1998) or (Smith et al., 1998) etc. (all authors should be included in the full list).

In the reference list, entries for journals [abbreviated in the style of Chemical Abstracts (the abbreviations Acta Cryst., J. Appl. Cryst. and J. Synchrotron Rad. are exceptions)], books, multi-author books, computer programs, personal communications and undated documents should be arranged alphabetically and conform with the following style:

Brünger, A. T. (1992a). X-PLOR. Version 3.1. A System for X-ray Crystallography and NMR. Yale University, Connecticut, USA.

Brünger, A. T. (1992b). Nature (London), 355, 472–474.

Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763.

Crowther, R. A. (1972). The Molecular Replacement Method, edited by M. G. Rossmann, pp. 173–178. New York: Gordon and Breach.

International Union of Crystallography (1999). (IUCr) Crystallography Journals Online, //journals.iucr.org .

International Union of Crystallography (2001). (IUCr) Structure Reports Online, //journals.iucr.org/e/journalhomepage.html .

Sheldrick, G. M. (2003). Acta Cryst. D59. In the press.

Yariv, J. (1983). Personal communication.

Note that inclusive page numbers must be given.

Identification of individual structures in the paper by use of database reference (identification) codes should be accompanied by a full citation of the original literature in the reference list. However, in tables containing more than ten such reference codes, citation in the reference list is not required.

11. Evaluation criteria

The information required in manuscripts is given below.

11.1. Crystallization data

A list of data recommended for inclusion in Crystallization Papers can be found on the web at //journals.iucr.org/d/services/crystallization/ .

11.2. Resolution

The effective resolution should be described clearly. Values of the internal agreement of the data, R_merge, together with the multiplicity (i.e. the average number of measurements for each reflection from which R_merge is calculated), the percentage of data with I > 3σ(I) and percentage completeness of the data are required for the overall data set and the highest resolution shell together with the limits of that shell in Å. For high-quality data obtained with synchrotron radiation, values of R_merge < 20%, completeness > 93% and observable data > 70% should be achievable for the highest resolution shell. A complete table listing the above criteria as a function of resolution should also be submitted, but will normally be included in the supplementary material, see §13.

11.3. Unrefined structures

Adequate experimental details should be provided to convince referees that the interpretation is correct, within the resolution of the analysis. If heavy-atom derivatives were used, sufficient data should be provided for evaluation of the quality of those derivatives. The fit of the model to the electron-density maps used to determine the structure should be shown or described by quantitative indicators, such as real-space residuals.

11.4. Refined structures

For refined structures the data required depend on the effective resolution of the analysis. The following should be included.

A final Ramachandran plot is important and should be provided for review purposes. The paper should include a brief statement of the percentage of amino acids in allowed, additionally allowed and disallowed regions of the plot.

The r.m.s. deviations in B values within each residue's main-chain and side-chain atoms should be included.

The crystallographic R index should be tabulated as a function of resolution and R_free should also be included.

Adequate details should be provided regarding the steps followed in constructing the model and refining the structure. Also requested are: the number of solvent atoms; solvent B values; the history and salient details of the refinement methods employed, including the resolution ranges that were used at various stages of refinement; the restraints used; a description of how the thermal parameters were treated; and how the solvent sites were selected and handled during refinement. It should be clear if van der Waals distances were restrained.

Hydrogen-bonding patterns within the protein should be described including the number of hydrogen-bond donors not involved in hydrogen bonding and any unsatisfied buried main-chain hydrogen bonds.

Any structural features that are considered somewhat unusual should be described. Examples include cis peptide bonds; unoccupied volume inside the protein, buried charge groups that are not involved in salt bridges or reasonable hydrogen-bonding environments; unusual locations of glycine and proline residues; unusual distributions of polar and hydrophobic groups within the molecule; and unusual bond lengths, bond angles, planes, intra- and intermolecular contacts.

12. Small-molecule structure determinations

Papers that report the results of crystal structure determinations of small molecules must report the associated experimental data as required in Notes for Authors for Section C of Acta Crystallographica. These data should be supplied as a single electronic file in CIF format. The CIF will be checked in Chester for internal consistency.

13. Supplementary publication procedure (deposition)

13.1. Purpose and scope

Parts of some papers are of interest to only a small number of readers, and the cost of printing these parts is not warranted. Arrangements have therefore been made for such material to be made available from the IUCr electronic archive via Crystallography Journals Online or to be deposited with the Protein Data Bank , the Nucleic Acid Database and the ICDD as appropriate.

13.2. IUCr electronic archive

All material for deposition in the IUCr electronic archive should be supplied electronically.

Non-structural information, which may include:

• details of the experimental procedure;

• details of the stages of structure refinement;

• details of mathematical derivations given only in outline in the main text and in mathematical Appendices;

• lengthy discussion of points that are not of general interest or that do not lead to definite conclusions but that do have significant value;

• and additional diagrams,

should be supplied in one of the formats given in §3.9.

Structural information (for small-molecule structures) should be supplied in CIF format; structure factors should be supplied as .fcf files.

13.3. Macromolecular structures

Authors should follow the deposition recommendations of the IUCr Commission on Biological Macromolecules [Acta Cryst. (2000), D56, 2 ]. For all structural studies of macromolecules, coordinates and structure factors must be deposited with the Protein Data Bank or the Nucleic Acid Database if a total molecular structure has been reported. Authors must supply the Protein Data Bank/Nucleic Acid Database reference codes before the paper can be published.

13.4. Crystallization data

For Crystallization Papers, authors are recommended to deposit their data with the relevant database.

14. Powder diffraction data

Authors of powder diffraction papers should consult the notes provided at the online CIF help page (//journals.iucr.org/c/services/cifhelp.html ). For papers that present the results of powder diffraction profile fitting or refinement (Rietveld) methods, the primary diffraction data, i.e. the numerical intensity of each measured point on the profile as a function of scattering angle, will be deposited.

15. Crystallography Journals Online

All IUCr journals are available on the web via Crystallography Journals Online; //journals.iucr.org/ . Full details of author services can be found at //journals.iucr.org/d/services/authorservices.html.

15.1. Electronic status information

Authors may obtain information about the current status of their papers at //journals.iucr.org/services/status.html .

15.2. Proofs

Proofs will be provided in portable document format (pdf). The correspondence author will be notified by e-mail when the proofs are ready for downloading.

15.3. Reprints

After publication, the correspondence author will be able to download the electronic reprint of the published article, free of charge. Authors will also be able to order printed reprints at the proof stage.