...or their colleagues and/or mentors. Disney's First Law ("Wishing will
make it so") does not apply to crystallography.
On 9/7/2016 11:10 AM, Green, Todd Jason wrote:
> 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
>>
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