Dear Kavyashree, I expect that you have a low-occupancy cadmium ion bound. If your resolution is not too low, say better than 2.5 Å, I would try to refine the occupancies of all cadmium ions. They are so big that it should work. If this does not work, you can make a rough estimate of the occupancy by using the scroll button in coot. If the electron density of the "regular" cadmiums disappears at say 3 sigma, and of your high-Bfactor cadmium disappears at 1 sigma, you could set the occupancy of the latter to 0.3 and see how the cadmium behaves during refinement. At low resolution occupancies and Bfactors are to a certain extend linked, and errors in your estimate of the occupancy will be compensated by the Bfactor.
Good luck, Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ka...@ssl.serc.iisc.ernet.in Sent: Wednesday, May 11, 2011 11:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] High B-factor for metal Dear users, I have refined a structure in R3 with cadmium bound to it, which was present in the crystallization condition. There are 2 chains in the asu. The structure is twinned. R and Rfree is around 22% and 28%. One of the cadmium has extremely high B-factor of 127, I tried replacing it with water, but there were positive peaks appearing after refinement, no other components in the protein buffer or crystallization condition fit there. and there are 2 glutamate residues in the interaction distance of "X" that come in that position. So kindly suggest me whether I need to continue with cadmium ion assuming that its occupancy is low, or any other options are there? Thanking you With regards M. Kavyashree -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
