Dear John,
Yes, I think the PDB should be stricter. The PDB is in the position to enforce compliance with rules and if they are not followed then one doesn't get a validation report and in turn it would be difficult to publish (most journals require a validation report). For years it has been tried to make adherence to standards voluntary but there are still examples, like the one that started the discussion, where people just don't bother. For these particular structures I actually suspect that even if there were all reports given to the referees they may not have looked carefully enough. The journal where they were published in is heavy on the chemistry side so perhaps the referees focused on the synthesis of the compounds rather than the structure and the interaction within the protein. Aside from that, at a resolution of 2.7A to 3A discussing detailed chemical interactions and placing a compound with confidence is questionable anyway. Cheers M ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of John Berrisford <j...@ebi.ac.uk> Sent: 22 July 2019 22:23:47 To: ccp4bb Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 Dear Harry We will be shortly making it mandatory for depositors to provide a value for at least one of the merging statistics (Rmerge, Rpim, CC1/2 etc..). Most depositors do, but we want to ensure that all depositors do provide at least one value for a merging metric. We would welcome feedback if we should be stricter and require a (or more than one) specific metric (e.g. CC1/2) – please be aware that any required metric must be available from all merging/scaling software. Thanks John From: CCP4BB <hrp-ccp...@virginmedia.com> Sent: 22 July 2019 11:32 To: John Berrisford <j...@ebi.ac.uk> Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 Hi John These are great, but the things that make me suspicious are the values of overall R(merge); these are tucked away in the full reports, rather than highlighted with all the other structural metrics in the validation sliders. It would be wonderful to be able to see at a glance where overall R(merge) values like these fit in with those of other deposited structures (even better if it could be drawn to the attention of authors before final deposition). Kay and Gérard have already pointed out that the data processing here may have some issues. Of course, those of us involved in teaching data processing have been emphasizing the importance of CC(1/2) rather than relying on R(merge) for yonks, but if CC(1/2) isn't given in the report it's all we have to go Harry -- Dr Harry Powell On 22 Jul 2019, at 10:05, John Berrisford <j...@ebi.ac.uk<mailto:j...@ebi.ac.uk>> wrote: Dear Daniel The issues you mentioned are highlighted in the wwPDB validation report http://www.ebi.ac.uk/pdbe/entry-files/6mo0_full_validation.pdf and global issues with the entry are highlighted in the validation sliders http://www.ebi.ac.uk/pdbe/entry/pdb/6MO0 The validation sliders are shown on the entry pages at all wwPDB PDB sites (RCSB, PDBe and PDBj) and they all provide a link to download the wwPDB validation report directly from the entry page. Regards John From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Bonsor, Daniel Sent: 19 July 2019 18:43 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 Would it be possible to add a public annotations section to the PDB, to allow us to potentially flag/warn whoever downloads that particular structure, there could be something wrong with it, such as wrong space group, no/poor density fitting for ligand. Something similar to PubPeer maybe? Daniel A. Bonsor PhD Institute of Human Virology, University of Maryland at Baltimore 725 W. Lombard Street N571 Baltimore MD 21201 ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Patrick Loll <pjl...@gmail.com<mailto:pjl...@gmail.com>> Sent: Friday, July 19, 2019 1:17 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 The idea of contacting the editor (and/or author) is an excellent one, and indeed the correct thing to do scientifically. However, I’m disillusioned: I’ve been down this path before with a high-profile vanity journal, and while the editors paid lip service to the notion that the record should be corrected, in reality they led me on for the better part of a year, and got me to write up detailed analyses of why the ligand positioning was not justified, before eventually saying “no, we don’t see any need to publish a correction.” I speculate that the journal prefers not avoid corrections, for fear that too many corrections will make the journal a less desirable destination. > On 19 Jul 2019, at 11:23 AM, Bärbel Blaum > <baerbel.bl...@intherabio.com<mailto:baerbel.bl...@intherabio.com>> wrote: > > Hi Rhys, > the reported B-factors for the “ligands” are all way below the reported > B-factors for the protein chains, with the worst of the three complexes > reporting unitless numbers 23.2 and 64.8, respectively, just to highlight > *one* striking feature of the data collection and refinement table. So even > with the limited info normally available to reviewers this table should have > raised a red flag. After the re-refinement suggested by others, i.e. your own > proper assessment of the crystallographic data, if you do not find noteworthy > density you may want to contact the article’s editor with your results. If > you work in this field, i.e. really care about this paper scientifically and > you are not afraid to confront the authors you could suggest writing a > comment/direct response article but in my opinion that would only make sense > if you can be sure beforehand that it will be linked visibly to the actual > paper, else it will be a waste of time. And don’t forget that just because > one or some of the authors did a bad job at the crystallographic end other > findings of the paper might still be solid – in collaborations often one > author is unable to critically evaluate another author’s contribution and > this would not be the first case were good synthetic or biological work is > presented along with a bad crystal structure. > By the way and a bit ironically this protein may have suffered bad > crystallography/scientific practice before - I think it was one of the fake > Krishna Murthy structures, right? The associated (now retracted) article I > mean is here > https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub [https://ars.els-cdn.com/content/image/S00222836.gif]<https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub> RETRACTED: Crystal structure of dengue virus NS3 protease in complex with a bowman-birk inhibitor: implications for flaviviral polyprotein processing and drug design - ScienceDirect - ScienceDirect.com | Science, health and medical journals, full text articles and books.<https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Dihub> www.sciencedirect.com<http://www.sciencedirect.com> COMMUNIC Crystal Structure of Dengue Complex with a Bowman-Bir ro L. 1Center for Macromolecular C f A 8 U T MCLM 244, Birmingham AL 35294-0005, USA 2Department of Biochemistry and Molecular Biology, Kansas University Medical Center 3901 Rainbow Boulevard Kansas City, KS 66160- 7421, USA Dengue viruses are members of the Flaviviridae and cause dengue fever Dengue fever and dengue hemorrhagic ... > Kind regards, Bärbel > --- > Bärbel Blaum, PhD > Inthera Bioscience AG > Einsiedlerstrasse 34 > CH-8820 Waedenswil > Switzerland > E-Mail: baerbel.bl...@intherabio.com<mailto:baerbel.bl...@intherabio.com> > Phone: +41 43 477 94 72-- > > > > Von: CCP4 bulletin board > <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> im Auftrag von "Manfred > S. Weiss" > <manfred.we...@helmholtz-berlin.de<mailto:manfred.we...@helmholtz-berlin.de>> > Antworten an: "Manfred S. Weiss" > <manfred.we...@helmholtz-berlin.de<mailto:manfred.we...@helmholtz-berlin.de>> > Datum: Freitag, 19. Juli 2019 um 16:03 > An: <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> > Betreff: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 > > Hi Rhys, > > all three structures are at modest resolution and they don't seem to > be properly refined. At least they are all below average. I wonder > how this paper made it past the referees. > > I haven't checked the paper, but there are ways and means how to > deal with weakly bound ligands in the best possible way. One aspect > is to improve the phases as much as possible without having the ligand > present. This was obviously NOT done. Another way is to use the > PANDDA approach, which relies on having many data sets available. > I suppose that this was also not done. > > The best way to check is to delete the ligand and so some extensive > refinement in order to remove the phase bias introduced by the > ligand. Only then you can reliably assess whether something is there > or not. > > Cheers, Manfred > > Am 19.07.2019 um 15:21 schrieb Rhys Grinter: >> Hi All, >> >> I was chatting with a colleague during a recent synchrotron visit and they'd >> recently come across some ligand/drug bound structures associated with a >> paper recently published in a high impact factor journal. >> >> They had pulled the associated SFs from the PDB and found that the electron >> density associated with these ligands didn't match that reported in the >> paper and certainly wasn't sufficient to model the alleged ligand. >> >> I also pulled the structure factors and after refinement in the >> presence/absence of the alleged ligand I also feel that the density present >> does not warrant modelling of the ligand. >> >> I was hoping that the community might be able to give me an outside opinion >> on these datasets (PDB IDs: 6MO0, 6MO1, 6MO2) and if the problem associated >> with the data is verified, provide some advice on how to proceed. >> >> This isn't the first occasion I've seen ligand bound structures with >> questionable density deposited in association with papers in well respected >> journals. Despite improvements to validation I feel that this problem is >> widespread. >> >> Best Regards, >> >> Rhys >> >> -- >> Dr Rhys Grinter >> NHMRC Postdoctoral Researcher >> Monash University >> +61 (0)3 9902 9213 >> +61 (0)403 896 767 >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 >> > > > -- > Dr. Manfred S. Weiss > Macromolecular Crystallography > Helmholtz-Zentrum Berlin > Albert-Einstein-Str. 15 > D-12489 Berlin > Germany > > > Helmholtz-Zentrum Berlin für Materialien und Energie GmbH > > Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren > e.V. > > Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta > Koch-Unterseher > Geschäftsführung: Prof. Dr. Bernd Rech (Sprecher), Prof. Dr. Jan Lüning, > Thomas Frederking > > Sitz Berlin, AG Charlottenburg, 89 HRB 5583 > > Postadresse: > Hahn-Meitner-Platz 1 > D-14109 Berlin > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjl...@gmail.com<mailto:pjl...@gmail.com> pj...@drexel.edu<mailto:pj...@drexel.edu> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. 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