Dear Silvia,
In addition to your high-B values I would also worry about your high
R/R-free values - I suggest running your dataset through xtriage to
check for twinning (or look carefully at the output of your data
processing - it should also include some checks for twinning).
The B-value estimated from the Wilson Plot would also be useful.
Best regards,
Pedro
Às 14:58 de 04/01/2021, Napolitano Silvia escreveu:
Dear Eleanor,
Thank you for your answer. You are right, I totally forgot to provide
this information.
The resolution is lower than 3 (2.19) Angstrom.
Attached is the run log of the last refinement. I hope that now it
will be clearer!
Best
Silvia
Silvia Napolitano
ETH Zurich
Institute of Molecular Biology and Biophysics
Otto-Stern-Weg 5, HPK E14
CH–8093 Zurich
Phone: +41 44 6332482
------------------------------------------------------------------------
*Da:* Eleanor Dodson <eleanor.dod...@york.ac.uk>
*Inviato:* lunedì 4 gennaio 2021 15:43:03
*A:* Napolitano Silvia
*Cc:* CCP4BB@JISCMAIL.AC.UK
*Oggetto:* Re: [ccp4bb] B-factors very high
Well - you dont give the resolution of your data or the "wilson B"
which will be recorded in the data processing log.
If the resolution is 3A or less a) it is hard to refine a B value, and
b) it certainly should be high..
So more information is needed.
Eleanor
On Mon, 4 Jan 2021 at 14:39, Silvia Napolitano
<silvia.napolit...@mol.biol.ethz.ch
<mailto:silvia.napolit...@mol.biol.ethz.ch>> wrote:
Dear CCP4 Community,
I am currently working on the structure of a monomeric protein of
23KDa. The protein is generally quite "loopy" and I think I am
mid-way refinement.
At the moment I am struggling, among other things, with an
extremely high B-factor and I'm not sure how to lower it.
Do you have any suggestions on how I can proceed to obtain a lower
average B-factor? (I am sorry if the question is rather naive, but
I have worked very little on X-ray structures so far)
I attached a screenshot of the polygon obtained from the last
refinement (the geometry now should be a bit improved, I am
running a new job at the moment). I will be happy to provide
further files if needed.
Many thanks in advance for your precious help!
I wish you a nice start to the new year.
Best
Silvia
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