Dear Randy,
Congratulations for this terrific piece of work!
As James Fraser was writing two days ago, this case establishes a
new paradigm for the "peer review" of structural papers :-) .
With best wishes,
Gerard.
--
On Fri, Sep 09, 2016 at 12:20:53PM +0100, Randy Read wrote:
> Dear all,
>
> Following on from Paul’s suggestion that the space group is wrong, I thought it might be interesting to try to solve this structure from scratch, using what I’m currently teaching students at a CCP4 workshop. What worked was to find some distant homologues with HHpred (top 3 hits after ignoring 5gnn), make a trimmed ensemble, and search with that. This gave a very clear solution for one molecule in P65. Model completion from that point works really well, given the resolution, using either phenix.autobuild or ARP/wARP.
>
> For the edification of the members of the BB, the ARP/wARP model is attached! (Hopefully no flames for an attachment of 135kB…) This model hasn’t had some really obvious rotamer fixes or extensions of the termini applied, but it has good stereochemistry, and R/Rfree are 0.241/0.285.
>
> Given the vastly improved statistics for a different space group and the huge differences in the model, it is to be hoped that the authors retract the original publication and PDB entry. Thanks to Gerard for pointing out the issues with this!
>
> Best wishes,
>
> Randy Read
>
>
>
> -----
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road E-mail: [log in to unmask]
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>
> > On 7 Sep 2016, at 16:51, Paul Adams <[log in to unmask]> wrote:
> >
> > Dear Gerard,
> >
> > thanks for pointing this structure out. This is indeed very startling. The paper indicates that the structure was refined with Phenix. However, if I download the model/data and refine (with Phenix) the starting R-factors are 0.36/0.38 and these get worse during refinement. Clearly the deposited model is not consistent with the R-factors reported in the paper, or in the wwPDB. In addition, analysis of the data suggests strongly that the true symmetry is P6 (possibly with a screw axis) - I suspect that this is the genesis of statements about twinning, but it isn’t clear if that was used in the refinement. Being charitable I can imagine that the wrong model was deposited in the wwPDB. However, this doesn’t explain the R-factors reported by the wwPDB, or the less than convincing images of the structure shown in the paper. I very much agree with you that there must have been ample alarms sounded along the way. It is cautionary that this wasn’t caught at some point. For me this highlights that the issues go beyond the naivety or impatience of a single student.
> >
> > Cheers,
> > Paul
> >
> >> On Sep 7, 2016, at 7:20 AM, Gerard Bricogne <[log in to unmask]> 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
> >>
> >> --
> >>
> >> ===============================================================
> >> * *
> >> * Gerard Bricogne [log in to unmask] *
> >> * *
> >> * Global Phasing Ltd. *
> >> * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
> >> * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 *
> >> * *
> >> ===============================================================
> >
> > --
> > Paul Adams
> > Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
> > Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
> > Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> > Vice President for Technology, the Joint BioEnergy Institute
> > Laboratory Research Manager, ENIGMA Science Focus Area
> >
> > Building 33, Room 347
> > Building 80, Room 247
> > Building 978, Room 4126
> > Tel: 1-510-486-4225, Fax: 1-510-486-5909
> > http://cci.lbl.gov/paul
> >
> > Lawrence Berkeley Laboratory
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> > BLDG 33R0345
> > Berkeley, CA 94720, USA.
> >
> > Executive Assistant: Louise Benvenue [ [log in to unmask] ][ 1-510-495-2506 ]
> > --
