The correspondence below captures a lively scientific debate on the best practices for accurate analysis of x-ray crystallography data. In the course of handling this correspondence, I solicited comments from a number of external reviewers who generously helped me navigate these waters and I wish to thank them for their time and efforts. The consensus of these experts is clear that the quality of the data and the level of noise within the electron density map in the Salunke study preclude tracing peptide residues within the x-ray crystal structures.
This debate has underscored the need to improve the rigor of the review process for manuscripts that include x-ray crystallography data. For many years, The Journal of Immunology has required that authors of manuscripts containing high-resolution structural data deposit those data in the Protein Data Bank (PDB) at the time of manuscript submission, and to include the PDB accession number in the published article. As a result of the correspondence below, The Journal of Immunology now requires that the PDB Summary Validation Report (available only recently) be included with submission of the manuscript so that it is available to editors and reviewers during the review process. This additional requirement will allow a thorough vetting of the authors’ interpretation of x-ray crystallographic data by expert reviewers, with the goal of eliminating ambiguity in the protein structures contained within published articles in the future.
We hope that publishing this correspondence and the journal’s response to the issues it exposes will stimulate discussion in the community of structural biologists and lead to constructive changes in the way crystallographic data are reviewed and interpreted in the future.