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Deposition of structural data redux

It has been almost exactly ten years since the publication of a “revolutionary” suggestion that macromolecular coordinates resulting from crystallographic and NMR studies should be deposited in the Protein Data Bank (PDB) and released immediately upon publication of the relevant papers. IUCr implemented a new policy in 2000 that disallows coordinate holds beyond the date of publication, while allowing a six-month hold on the structure factors. That policy is mandatory for the IUCr journals and provides a template for policies of almost all other journals that publish macromolecular structures, as well as for funding bodies such as NIH or HHMI.

The availability of structure factors is particularly important if there could be any doubts about the correctness of the reported structures. A recent fiasco related to the inverted structure of the proteins MsbA and EmrE provides a very good example. A number of coordinate data sets deposited in the PDB were not accompanied by structure factors, so other scientists could not perform any verification of the models that turned out to be seriously wrong.

Whether enforced or not, the policy of depositing the structure factors (with a possible six-month hold) is already on the books. When a paper is already published, it is unlikely that the availability of structure factors could really hurt the competitiveness of the authors, unless there was a problem that could be detected by others. But that is exactly why these data should be generally available!

I would thus like to make a number of suggestions directed to authors, journals, funding bodies, the IUCr and the PDB. First, I feel that the PDB should not accept deposition of coordinates not accompanied by structure factors. Second, the journals should be much more vigilant in enforcing the rules regarding deposition of structural data. However, I strongly urge the IUCr to reconsider and revise its current policy that allows six-month hold of the structure factors, and instead to treat them exactly in the same way as the coordinates. The PDB should become much more active in assuring the scientific community that the coordinates and structure factors in their repository are accurate, properly annotated and fully cross-referenced to their respective publications. Let us remember that many of the current depositors might be proficient in running crystallographic programs, but have little or no understanding of crystallography as such. Even more important is the fact that major consumers of the coordinates are not structural biologists, but experts in other fields.

To summarize, much has changed during the last ten years and the policies that were adequate then seem no longer to benefit the scientific community in the same way. Thus, time has probably come to take another look at them, and modify them accordingly. The IUCr is the right organization to initiate such a change, but the journals and funding agencies might wish to act even sooner. I hope that my proposal, controversial as it might appear to some (as was the previous one ten years ago), could be a basis of starting a thorough discussion of this important matter.

Alex Wlodawer

An expanded version of this letter with interesting, amusing and provocative details appears in Acta Cryst. (2007), D63, 421-423.