Much of the analysis suggested, like checking B-factors of neighboring
atoms, coordination geometry and atom-atom distances, are implemented here:
https://cmm.minorlab.org/metal_sites
Engin
On 9/8/22 8:27 AM, Eleanor Dodson wrote:
Is that the right way round? Atomic no K 19, Na 11
Call something K when it should be NA - B factor will shoot to reduce
the atom contribution.
Call something Na when it should be K - B factor will become very small..
As you say - check which fits best with the surrounding atoms..
On Thu, 8 Sept 2022 at 14:16, Jon Cooper
<0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
Hello, K will always have a higher B-factor for a given piece of
density due to it having a larger atomic number. Is the K B-factor
much higher than those of neighbouring atoms and, if not, it's
probably the best interpretation? Cheers, Jon.C.
Sent from ProtonMail mobile
-------- Original Message --------
On 8 Sep 2022, 14:07, smita yadav < sm...@rcb.res.in> wrote:
Dear Community,
Can you tell me. if we fit some metal
in X-ray structure and its geometry and other properties are
satisfied but showing some higher B-factor. does it validate
to put that metal-ligand.ligand. At one site 2 metals such as
K and NA fit, but K shows a higher B-factor, but other
parameters such as geometry and other fit better for K instead
of NA. So, out of the two ligands at the same site which one
would be more favorable to be fit.
--
On Thu, Sep 8, 2022 at 6:35 PM smita yadav <sm...@rcb.res.in>
wrote:
Dear Community,
Can you tell me. if we fit some
metal in X-ray structure and its geometry and other
properties are satisfied but showing some higher B-factor.
does it validate to put that metal-ligand.ligand. At one
site 2 metal such as K and NA fits, but K shows higher
--
Regards,
Smita Yadav
Ph.D SRF
Regional Centre for biotechnology,
Haryana-121001.
--
Regards,
Smita Yadav
Ph.D SRF
Regional Centre for biotechnology,
Haryana-121001.
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--
Engin Özkan, Ph.D.
Associate Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu
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