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
>
>
>
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