Wouldn't it be possible to estimate the occupancy of the Cd-ions from
the peak heights of a DANO-map. Especially useful if there is doubt
about the presence of Cd at this "low occupied site".
Cheers, Georg
Am 11.05.11 11:33, schrieb herman.schreu...@sanofi-aventis.com:
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
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Universität Tübingen
Interfakultäres Institut für Biochemie
Dr. Georg Zocher
Hoppe-Seyler-Str. 4
72076 Tuebingen
Germany
Fon: +49(0)-7071-2973374
Mail: georg.zoc...@uni-tuebingen.de
http://www.ifib.uni-tuebingen.de
