Even though PDB-REDO cannot salvage this model without extensive rebuilding which is what Tristan showed, it is fun to look at the maps and B-factors near the ligand. The B-factors go way up and the negative difference density disappears, as does most of the 2mFo-DFc density. It’s obviously not news to most people on the CCP4BB, properly refining B-factors is really important!
Cheers, Robbie From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bärbel Blaum Sent: Friday, July 19, 2019 17:24 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 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. 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