----------Individual ADP refinement----------
R-FACTORS <Bi-Bj> <B> WEIGHT TARGETS
work free delta data restr
28.36 32.91 4.55 14.984 101.982 0.079 5.042
28.25 33.03 4.78 14.788 103.837 0.079 5.023
min max mean <Bi,j> iso aniso
Overall: 47.49 211.88 96.79 10.75 2956 2930
Protein: 47.49 211.88 96.79 10.75 2930 2930
Water: 63.50 130.55 88.98 N/A 19 0
Other: 109.20 140.77 117.24 N/A 7 0
Chain A: 74.14 153.67 99.01 N/A 1474 1474
Chain C: 109.20 140.77 117.24 N/A 7 0
Chain B: 47.49 211.88 94.54 N/A 1456 1456
Chain S: 63.50 130.55 88.98 N/A 19 0
at this point I would def. look at the pointless and xtriage outputs...
Dr. Matthias Barone
AG Kuehne, Rational Drug Design
Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284
________________________________
From: CCP4 bulletin board <[email protected]> on behalf of Eleanor Dodson
<[email protected]>
Sent: Monday, January 4, 2021 4:16:05 PM
To: [email protected]
Subject: Re: [ccp4bb] B-factors very high
Hmm - this is extracted from your log file: it looks more sensible..
2899: b_iso_mean = 66.62
2907: b_iso_min = 63.50 (limit = 1.00)
2908: b_iso_max = 68.13 (limit = 80.00)
2909: b_iso_mean = 66.62
The average B is 66??
I am more familiar with REFMAC and the fact that the iso_min and iso_max are
so close looks odd to me, but maybe that is a PHENIX quirk?
But you need to look at the data processing log if you have access to it.
The CCP4I2 gives a very useful analysis of your data..
Eleanor
On Mon, 4 Jan 2021 at 15:03, Barone, Matthias
<[email protected]<mailto:[email protected]>> wrote:
dear silvia,
apart from the resolution, it would be good to know your current refinement
strategy and if you fed the structure to pdbredo yet. How did that turn out?
the polygon values are picked from structures at similar resolution afaik. In
any case, a better list of B-factors is the one you find in the refinement tab
"Atomic properties", where phenix lists them for the macromolecules and ligands
separately. In that tab you will also find a list of which atoms cause such
high ADPs. I think Eleanor is talking about such a screenshot
best, matthias
Dr. Matthias Barone
AG Kuehne, Rational Drug Design
Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin
Germany
Phone: +49 (0)30 94793-284
________________________________
From: CCP4 bulletin board <[email protected]<mailto:[email protected]>>
on behalf of Eleanor Dodson
<[email protected]<mailto:[email protected]>>
Sent: Monday, January 4, 2021 3:44:33 PM
To: [email protected]<mailto:[email protected]>
Subject: Re: [ccp4bb] B-factors very high
That polygon is not very useful I dont think. The statistics need to be given
separately for structures solved at given resolutions.
Eleanor
On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson
<[email protected]<mailto:[email protected]>> wrote:
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
<[email protected]<mailto:[email protected]>>
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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