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> On Behalf Of Bonsor, Daniel Sent: 19 July 2019 18:43 To: 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, Im disillusioned: Ive 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 dont 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 articles 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 dont 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 authors 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%3Dih ub <https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Di hub> <https://www.sciencedirect.com/science/article/pii/S002228360093924X?via%3Di hub> 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. 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 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &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 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &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 <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
