Hi Catherine, Is the temperature factor for the Fe sensible? I have seen their value for metal ions rise to unrealistically high values during refinement.
Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email [email protected] tel 01235 567717 ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Firdous Tarique <[email protected]> Sent: 05 September 2025 11:15 To: ccp4bb <[email protected]> Subject: Re: [ccp4bb] Green density over Fe in heme Hi Try putting water molecule into this green density. It is often reported for redox protein where water molecule is bonded to heme through u oxo bridge. OR there it is a binuclear catalytic center with additional metal ion such as Fe or Zn linked with heme center through water molecule..kindly see pdb id: 8bgw for more information. Best wishes Firdous On Fri, 5 Sept 2025, 10:40 Catherine Back, <[email protected]<mailto:[email protected]>> wrote: Good morning, I am currently solving a structure containing four heme b molecules (res 1.7 Å), each coordinated by two histidines. The refinement is looking good, but the output from refinement has marked the Fe ions of each heme with positive density (green) in the FoFc difference map - see image. Any ideas why? I used the Monomer Library in Coot to add hemes ('HEM') in. Is it something to do with the oxidation state of the Fe? And if so, is there anything I can do about it? Best wishes, Catherine Dr Catherine R. Back (she/her) Senior Post-doctoral Research Associate School of Biochemistry University of Bristol UK ________________________________ 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 email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm. ######################################################################## 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/
