Hi Stephen, What happens if you delete the CE methyl group and run a round of refinement. Do you get a positive blob of difference density in between the two sulfurs? Or looks everything pretty ok? In the first case you may indeed have some unusual phenomenon, in the latter case, the methyl group is probably not linked to the cysteine, but at some disordered, invisible position away from the cysteine. This would be the more usual (and boring) explanation.
Best, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Stephen Graham Gesendet: Mittwoch, 17. Juli 2019 16:03 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Bond between Cys S and Met methyl group? EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk Hi all, We've spotted something very weird in our density that we're struggling to reconcile...we have two sulfur atoms (from Met and Cys residues) that are very close together. The density looks for all the world like the methyl group from the Met should also be bonding to the Cys, although obviously the non-bonded terms are keeping them apart during refinement. The dmin is 1.72 and R/RFree are ~0.18/0.20 so the density should be pretty believable. We've seen the same in two crystals. Interestingly, we don't see much change in density if we process just the first/last quarter of the dataset so it isn't overly sensitive to radiation damage during collection. I posted a short vid on Twitter to illustrate: https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_i_status_1151488524425814016&d=DwIFAw&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=AGJpHgNJ7OJQ60bcbZONEofZkhRwnQqnDQtlX6xRQVY&s=10R2PgUMqqcCQ2fADadiNWCxz-zY9dt4V8mJt_oPSFE&e= Has anyone ever seen something like this? Is a (Cys)CA-CB-SG-CE-SD-CG-CB-CA(Met) bond possible? Thanks, Stephen -- Dr Stephen Graham Sir Henry Dale Fellow and University Lecturer Department of Pathology University of Cambridge Tennis Court Road Cambridge CB2 1QP https://urldefense.proofpoint.com/v2/url?u=http-3A__www.path.cam.ac.uk_research_investigators_graham_&d=DwIFAw&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=AGJpHgNJ7OJQ60bcbZONEofZkhRwnQqnDQtlX6xRQVY&s=1Wxlqn5ABBEZSTuhDIUatEkDPjr78DB_M6NHrD6xsyY&e= ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFAw&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=AGJpHgNJ7OJQ60bcbZONEofZkhRwnQqnDQtlX6xRQVY&s=LYaCXjAq5Bn667eSDfKBUcrZNF5vmt9FdUxnOiPJ-ps&e= ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
