Data science skills for referees: I Biological X-ray crystallography

TL;DR

This paper outlines essential data evaluation checks for referees in biological X-ray crystallography, emphasizing validation reports, model refinement, and potential reprocessing of diffraction data to ensure data integrity in structural biology publications.

Contribution

It provides a detailed guide for referees on how to assess underlying data in biological X-ray crystallography articles, including validation and reprocessing procedures, which is a novel focus for referee training.

Findings

Referees should review PDB validation reports for each structure.

Referees are encouraged to perform one cycle of model refinement.

Reprocessing diffraction data may be necessary for thorough evaluation.

Abstract

Since there is now a growing wish by referees to judge the underpinning data for a submitted article it is timely to provide a summary of the data evaluation checks required to be done by a referee. As these checks will vary from field to field this article focuses on the needs of biological X-ray crystallography articles, which is the predominantly used method leading to depositions in the PDB. The expected referee checks of data underpinning an article are described with examples. These checks necessarily include that a referee checks the PDB validation report for each crystal structure accompanying the article submission; this check whilst necessary is not sufficient for a complete evaluation. A referee would be expected to undertake one cycle of model refinement of the authors biological macromolecule coordinates against the authors processed diffraction data and look at the various validation checks of the model and Fo-Fc electron density maps in e.g. Phenix_refine and in COOT. If the referee deems necessary the diffraction data images should be reprocessed (e.g. to a different diffraction resolution than the authors submission). This can be requested to be done by the authors or if the referee prefers can be undertaken directly by the referee themselves. A referee wishing to do these data checks may wish to receive a certificate that they have command of these data science skills. The organisation of such voluntary certification training can e.g. be via those crystallography associations duly recognised by the IUCr to issue such certificates.