You can also look at your anomalous maps. For most
energies/wavelengths used to
collect protein data, f" for K will be just under 2x the f" for S
while for Na f"
will be much less (0.2-0.25 of S). So you can use S atom anomalous as
an internal reference.
If you see anomalous peaks at your S atoms, then you would also expect
peaks at
K atoms but not at Na atoms.
Regards,
Mitch
$ echo 'Atom Wave (keV) f"' ; for atom in NA S K ; do echo -e
NWAV 5 0.9 1 1.2 1.4 1.7"\n"ATOM $atom"\nEND\n"| crossec | awk
'NF==4&&$2+1>1{printf "%3s %6.2f %6.2f %8.4f\n", $1, $2, 12.39842/$2,
$4}'; done | sort -k2,2n -k4n
Atom Wave (keV) f"
NA 0.90 13.78 0.0411
S 0.90 13.78 0.1982
K 0.90 13.78 0.3948
NA 1.00 12.40 0.0512
S 1.00 12.40 0.2439
K 1.00 12.40 0.4819
NA 1.20 10.33 0.0746
S 1.20 10.33 0.3474
K 1.20 10.33 0.6770
NA 1.40 8.86 0.1023
S 1.40 8.86 0.4656
K 1.40 8.86 0.8979
NA 1.70 7.29 0.1507
S 1.70 7.29 0.6677
K 1.70 7.29 1.2685
Quoting Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
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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