Depending upon the amount of radiation exposure, the iron might be reduced (or more likely, in a mixed oxidation state) by the X-ray beam.
Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Nukri Sanishvili <sannu...@gmail.com> Sent: Monday, February 22, 2021 12:33 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure EXTERNAL MAIL Sorry, in my previous email I was oblivious to the fact that there was Fe. Iron is almost certainly oxidized. So, if you started collecting data with reduced iron, but it got oxidized during data collection, you are probably using the parametrization for the reduced rather than oxidized one in the refinement. I wonder if it is so and if going to the reduced state would make a difference. Best, N. On Mon, Feb 22, 2021 at 12:23 PM Pavel Afonine <pafon...@gmail.com<mailto:pafon...@gmail.com>> wrote: Hi, as others pointed out electron rich elements tend to amplify imperfections visible in Fo-Fc maps. Consider: - refining occupancy of Fe, the site may be partially occupied; - refining f' and f'' if data are anomalous; - surrounding histidines may 'see' this Fe as a nonbonded interaction and thus repulsion terms may kick in and push Fe from its position. Try defining weak coordination bonds between Fe and respective nitrogens; - refining anisotropic ADP of Fe only. Good luck! Pavel On Mon, Feb 22, 2021 at 7:27 AM Patrick Needham <needh...@miamioh.edu<mailto:needh...@miamioh.edu>> wrote: ________________________________ 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 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today. ######################################################################## 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/
