Hello,
Sorry to hijack this discussion, but does someone know if reduction of a disulphide could be a manifestation of radiation damage? Especially in cryoEM, since we're shooting electrons at it. One way to test this would be to do a rough zero-dose extrapolation (repeat motion correction with fewer and fewer frames, use the particle coordinates and orientations determined with the full dose to extract particle images and do reconstructions from the micrographs obtained with fewer frames) and see if this feature appears with accumulated dose. But this is tricky to do if motion correction is not perfect. At least according to the paper that introduced HexAuFoil grids: https://doi.org/10.1126/science.abb7927 ; but I don't know if anyone has tried even without these grids. Cheers, Guillaume ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Artem Evdokimov <artem.evdoki...@gmail.com> Sent: Monday, March 17, 2025 4:50:37 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Query Regarding Additional Density Near Disulfide Bond in Cryo-EM Structure To me this looks like a mixture of oxidized and reduced states of the S-S bond. Hard to say with any certainty seeing as the (optical) resolution is modest. Artem - Cosmic Cats approve of this message On Mon, Mar 17, 2025 at 8:18 AM Devbrat Kumar <devformed...@gmail.com<mailto:devformed...@gmail.com>> wrote: Hello Everyone, I am worried about the density of the disulfide bond in the cryo-EM structure that I am analyzing. The experimental map shows the expected density for the disulfide bond involving two cysteine residues, but in addition, I see some unexplained density, which I do not know how to interpret. I have attached the figure for your reference. Does anyone have experience with such extra density around a disulfide bond in their structures? Any thoughts would be greatly appreciated. Thanks for your attention and assistance. Warm regards Devbrat kumar Postdoctoral Fellow IITD, In ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ 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/
