[phenixbb] High B factors

Kay Diederichs Kay.Diederichs at uni-konstanz.de
Fri Jul 12 00:08:37 PDT 2019

Dear Sozanne,

I expect these data were collected at a synchrotron, and they are quite
weak at 2.5A? (would be good to know CC1/2 in the high-resolution shell)

If so, what you see is normal, and there's most likely nothing wrong
with your data or model. I've seen Wilson and average B-factors higher
than the ones you cite, for perfectly correct models and well-measured
data. It is just a fact that your protein's atoms vibrate in the
lattice, and the B factors are a way to measure how much.

There is a mathematical relation between B-factors and strength of
diffraction at high resolution; the higher the former, the lower the


On 7/11/19 6:49 PM, phenixbb-request at phenix-online.org wrote:
> Date: Thu, 11 Jul 2019 11:50:52 -0400
> From: ssolmaz <ssolmaz at binghamton.edu>
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] High B factors
> Message-ID:
> 	<CAHYfRfKKMViLmaEuVr0aANGu6iaW6ofMAWSKHZ5JuCnOusFQ4w at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> Dear all,
> We recently determined a protein structure by molecular replacement and the
> statistics are looking good, however, the average B-factor is unusually
> high, and the Wilson B-factor is high too.  A quick research on the subject
> suggested that high B-factors are acceptable as long as one has excluded
> and double-checked for other crystallographic problems. Which problems
> should I check for and what is your opinion on the high B-factor? Is there
> anything that could be done to lower it?
> Resolution: 2.5 A
> Space group P3121, 60.0 60.0 142.6 90 90 120
> R work 24.6%
> R free 26.4%
> Wilson B-factor 73.2
> Average B-factor 99.5
> Thank you for your advice,
> Best, Sozanne.
> Sozanne Solmaz, Ph. D.
> Assistant Professor of Biological Chemistry
> Department of Chemistry, State University of New York at Binghamton
> PO Box 6000, Binghamton, NY 13902
> Office: Smart Energy Building Room SN1045
> 25 Murray Hill Road, Vestal, NY, 13850
> http://chemiris.chem.binghamton.edu/SOLMAZ/solmaz.html

Kay Diederichs                http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs at uni-konstanz.de    Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

This e-mail is digitally signed. If your e-mail client does not have the
necessary capabilities, just ignore the attached signature "smime.p7s".

-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 5322 bytes
Desc: S/MIME Cryptographic Signature
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190712/afd3e821/attachment.p7s>

More information about the phenixbb mailing list