But are there two conformations of the disulphide? or one disulphide and one broken link? Eleaor
On Mon, 6 May 2024 at 20:42, Dr. Kevin M Jude <kj...@stanford.edu> wrote: > I have done this in shelxl or phenix refinement, you can define occupancy > groups (or free variables in shelxl) so that 472A and 384A are one group, > 472B and 384B are another. Pretty sure there is a similar solution in > refmac. Though also if the 384A rotamer doesn’t clash with the 472B > rotamer, you could have three states A/A (disulfide), A/B (no disulfide), > B/B (no disulfide). > > > > -- > > Kevin Jude, PhD > > Structural Biology Research Specialist, Garcia Lab > > Howard Hughes Medical Institute > > Stanford University School of Medicine > > Beckman B177, 279 Campus Drive, Stanford CA 94305 > > > > > > *From: *CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Liliana > Margent <lmarg...@gradcenter.cuny.edu> > *Date: *Monday, May 6, 2024 at 12:20 PM > *To: *CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject: *[ccp4bb] Modeling Disulfide Bond Occupancies > > Greetings everyone, > > I'm currently in the process of modeling a disulfide bond in two > structures. However, when I attempt to model single occupancy for the > cysteines involved in the bond, negative density blobs emerge within the > disulfide bond. This suggests the possibility of alternate conformations > for the cysteines. > > Yet, when I endeavor to model alternate conformations for both cysteines, > their occupancies do not align despite running refinement with a bond > parameter file that specifies the link. To illustrate, I initiate the > refinement with occupancies for Cys472 as A0.75/B0.25 and for C384 as > A0.75/B0.25, but post-refinement, the output occupancies appear as Cys472 > A0.84/B0.16 and for C384 A0.97/B0.03. Where A confs participate in the s-s > bond. > > Has anyone else encountered this issue before, or does anyone have > suggestions on how to refine these cysteines to achieve coherent > occupancies? > > Thank you for any insights you can provide. > > Best, > Liliana > > ######################################################################## > > 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/ > > ------------------------------ > > 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 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/
