Dear Kavyashree, Did you properly label the dual positions as alternate positions (same residue number and with A and B added just in front of the residue name)?. Also, did the occupancies sum up to less then 1, which makes perfect physical sense, or to more than 1? At 2.35 Å and with a partially occupied dual cadmium positions, you cannot expect miracles from the refinement programs. If the sum is more than 1, I would round off the occupancies to some sensible values with a sum of 1 and fix them for the rest of the refinement.
Best regards, Herman -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of [email protected] Sent: Wednesday, May 11, 2011 12:00 PM To: [email protected] Subject: Re: [ccp4bb] High B-factor for metal Dear Sir, The resolution is 2.35Ang. I was trying to refine Cadmium occupancy using the option of "SAD data directly" in refmac (as it cadmium gives anomalous signal at 1.54179 wavelength) and then use the obtained occupancy of those atoms to refine in usual way. It used to to refine occupancies of both cadmium and sulphur in (SO4) which is present in the structure, but 2 of the cadmium appears to have dual occupancy (which was confirmed as water added as a coordinate sphere used to come closer than 2.0 ang after refinement, so I tried giving 2 occupancies instead). After occupancy refinement as stated above, they were not summing up to 1, so I had doubts whether to continue this method or not. Thank you With regards M. Kavyashree > 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:[email protected]] On Behalf Of > [email protected] > Sent: Wednesday, May 11, 2011 11:30 AM > To: [email protected] > 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. > > -- > This message has been scanned for viruses and dangerous content by > MailScanner, and is believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
