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> > 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 > Kind regards, Bärbel > --- > Bärbel Blaum, PhD > Inthera Bioscience AG > Einsiedlerstrasse 34 > CH-8820 Waedenswil > Switzerland > E-Mail: baerbel.bl...@intherabio.com > Phone: +41 43 477 94 72-- > > > > Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> im Auftrag von "Manfred S. > Weiss" <manfred.we...@helmholtz-berlin.de> > Antworten an: "Manfred S. Weiss" <manfred.we...@helmholtz-berlin.de> > Datum: Freitag, 19. Juli 2019 um 16:03 > An: <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 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
