The PDB validation should flag issues as big as described here. (Did it in this case? It sounds very sketchy that the model should have such low R factors at the stated resolution with such big issues. It doesn’t add up IMO.) However, the authors are free to choose to ignore the validation report. The PDB is a repository, not a gatekeeper. Should it be a gatekeeper? I don’t know.
/Julia -- Dr. Julia Griese Associate Professor (Docent) Principal Investigator Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-75124 Uppsala Sweden email: julia.gri...@icm.uu.se<mailto:julia.gri...@icm.uu.se> phone: +46-(0)18-471 4982 Griese lab<https://www.uu.se/en/department/cell-and-molecular-biology/research/structural-biology/griese-lab> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of "Oganesyan, Vaheh" <vaheh.oganes...@astrazeneca.com> Reply to: "Oganesyan, Vaheh" <vaheh.oganes...@astrazeneca.com> Date: Monday, 2 June 2025 at 15:05 To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] How to address deposited structures poorly modeled? Hello, All suggestions on what and how to handle this case are good. However, aren’t we missing a major point? How could a model that exhibits gross disagreement with data be allowed in PDB? Isn’t validation protocol created to prevent cases like this? Vaheh From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Nikolas Sent: Friday, May 30, 2025 5:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to address deposited structures poorly modeled? *enters the BB and kneels in reverence* Dear BB, Recently, delving among papers and structures for a current project, I came across a deposited structure of interest that is terribly modeled. In the PDB resolution is 2.00 Å (R/Rfree=0.19/0.22) and the quality indicators are not terrible but upon opening it and checking the maps there are some severe mistakes in the modeling. For instance, a full chain that is in the negative Fo-Fc while positive density is present, some density that is quite clear for SO4 molecules (buffer) modeled as water and density for water molecules neglected. Some parts seem like “coot:runwater” has been used and not checked. The catalytic site is well defined. Now, I’ve started my journey in crystallography not too long ago and I’ve got many years, structures to solve and things to learn, and I know that sometimes the dataset “is what it is” but these seems quite big mistakes. Especially because I’ve worked with such proteins before and I know the systems. My question thus is: would it be right to contact the author of this structure and point to these issues? What’s the best way to address such things, possibly without coming off as obnoxious? Thank you for your wisdom. Cheers, Nikolas *bows and leaves the BB* ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
