or one of the 32 authors in this case!

________________________________________
From: CCP4 bulletin board <[log in to unmask]> on behalf of Roger Rowlett <[log in to unmask]>
Sent: Wednesday, September 7, 2016 10:07 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] Another puzzle: 5gnn

What this and similar examples suggest is that peer reviewers need
better tools to evaluate the quality of structures submitted for
publication. Authors should be vetting structures, but this is not
always happening. So it falls to reviewers to catch the problems.

Cheers,

_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [log in to unmask]

On 9/7/2016 10:20 AM, Gerard Bricogne wrote:
> Dear all,
>
>       While the thread on "Another MR pi(t)fall" is still lukewarm, and
> the discussion it triggered hopefully still present in readers' minds,
> I would like to bring another puzzling entry to the BB's attention.
>
>       When reviewing on Monday the weekend's BUSTER runs on the last
> batch of PDB depositions, Andrew Sharff (here) noticed that entry 5gnn
> had been flagged as giving much larger R-values when re-refined with
> BUSTER (0.3590/0.3880) than the deposited ones (0.2210/0.2500). This
> led us to carry out some investigation of that entry.
>
>       The deposited coordinates were flagged by BUSTER as having 4602
> bond-length violations, the worst being 205.8 sigmas, and other wild
> outliers. The initial Molprobity analysis gave a clash score of near
> 100, placing it in the 0-th percentile. The PDB validation report is
> dominantly red and ochre, with only a few wisps of green.
>
>       Examining the model and map with Coot showed "waters, waters
> everywhere", disconnected density, and molecules separated by large
> layers of water. The PDB header lists hundreds of water molecules in
> REMARK 525 records that are further than 5.0 Angs from the nearest
> chain, some of them up to 15 Angs away.
>
>       The cartoons on the NCBI server at
>
> http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=142582&dps=1
>
> show random coils threaded up and down through beta-strands, and the
> one on the RCSB PDB site at
>
>         http://www.rcsb.org/pdb/explore.do?structureId=5GNN
>
> also shows mostly random coil, with only very few and very short
> segments of secondary structure.
>
>       In reciprocal space, an oddness of a different kind is that if
> one looks at the mtz file, the amplitudes and their sigmas are on a
> very small scale. However the STARANISO display shows a smooth and
> plausible distribution of I/sig(I) to the full nominal resolution
> limit of 1.6A.
>
>       Looking at the publication associated with this entry
>
>               http://www.ncbi.nlm.nih.gov/pubmed/27492925
>
> indicates that the structure was solved by MR from a model obtained
> from a structure prediction server (I-TASSER). No further details are
> given, even in the Supplemental Material. Table 1 does report a
> MolProbity clash score of 103.59, as well as 10% Ramachandran outliers
> and 25.51% rotamer outliers. It also contains a mention of a twinning
> operator -h, -k, l with a twinning fraction of 0.5, although there is
> no mention of it in the text nor in the PDB file.
>
>       I will follow my own advice and resist the temptation of calling
> this "the end of civilisation as we know it", but this is startling.
> Perhaps we have over-advertised to the non-experts the few successes
> of structure prediction programs as reliable sources of MR models and
> thus created unwarranted optimism, besides the usual exaggeration of
> the degree to which X-ray crystallography has become a push-button
> commodity that can deliver results to untrained users. What is also
> disconcerting is that the abundant alarm bells that rang along the way
> (the MolProbity clash score and geometry reports, the contents of the
> PDB validation report, and simple common sense when examining electron
> density and model) failed to make anyone involved along the way take
> notice that there was something seriously wrong.
>
>       This case seems to bring to the forefront even more vividly than
> 4nl6 and 4nl7 some collective issues that we face. Here the problem is
> not one of contamination of a protein prep resulting in crystals of
> "the wrong protein": there is also a more diffuse contamination by
> deficiencies of judgement, expertise and vigilance at several
> consecutive stages, including refereeing and publication.
>
>       Validation is a hot topic at the moment, and this may serve as a
> concrete example that some joined-up thinking and action is indeed a
> matter of urgency, and that extreme scenarios of things going wrong do
> not exist solely in the imaginations of obsessive-compulsive/paranoid
> validators.
>
>       I am grateful to several colleagues for correspondance and
> discussions on the matters touched upon on this message.
>
>
>       With best wishes,
>
>            Gerard
>