Re: [ccp4bb] Temperature factor discrepancy

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Temperature factor discrepancy
From: Wim Burmeister wpb {- at -} EMBL {- dot -} FR
Date: 2008-12-03

I should have given the precision that the problem remains unaffected
by a change of the resolution range (even if I use for example only 4.5
to 3 A resolution).

I am not using TLS and the data are quite isotropic. Rcryst values are
as expected for such a structure.

Anopther 3.5 A dataset does not show the problem (right column).

cellpadding="0" cellspacing="0" width="529">

valign="top" width="189"> style="text-align: center; line-height: 150%;" align="center"> w:st="on">Wilson style="" lang="EN-GB"> plot B-factor [Å²]	valign="top" width="161"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">66	valign="top" width="180"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">43
valign="top" width="189"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">Refinement	valign="top" width="161"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">	valign="top" width="180"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">
valign="top" width="189"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">R_cryst	valign="top" width="161"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">0.186 (0.259)	valign="top" width="180"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">0.190 (0.239)
valign="top" width="189"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">R_free	valign="top" width="161"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">0.268 (0.408)	valign="top" width="180"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">0.256 (0.278)
style="text-align: center; line-height: 150%;" align="center"> style="font-size: 8pt; line-height: 150%;" lang="EN-GB">Rms deviations from ideal bondlengths (Å)	width="161"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">0.020	width="180"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">0.018
style="text-align: center; line-height: 150%;" align="center"> style="font-size: 8pt; line-height: 150%;" lang="EN-GB">Rms deviations from ideal bond angles (°)	width="161"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">2.0	width="180"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">1.9
style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">Average B-factor [Å²] style="font-size: 8pt; line-height: 150%;" lang="EN-GB">	width="161"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">39	width="180"> style="text-align: center; line-height: 150%;" align="center"> style="" lang="EN-GB">46

Values for
the highest resolution bin are given in brackets.

Cheers

Wim

Wim Burmeister a écrit :

Dear all,

I have a 3 A structure refined with REFMAC which gives consistently
average atomic B-factors of 40 A2, whereas the B factor from a Wilson
plot is about 60 A2. Is there any explanation for such a discrepancy?

There are no obvious problems:

No twinning, spacegroup P21 with two molecules in the asu, no proper
ncs symmetry. No pathologic Wilson plot, complete and redundant dataset
(although collected on several crystals with serious problems due to
radiation damage).

Interestingly, the Wilson plot of the Fcalc values is about 60 A2 as
for Fobs in the output dataset.

Yours

Wim

-- 
*******************************************************************************
Wim Burmeister
Professeur, Membre de l'Institut Universitaire de France
Unit of Virus Host Cell Interactions (UVHCI) UMR5233 UJF-EMBL-CNRS
6 rue Jules Horowitz
B.P. 181, F-38042 Grenoble Cedex 9          FRANCE
E-mail: wpb@embl.fr
Tel:    +33 (0) 476 20 72 82       Fax: +33 (0) 476 20 94 00
http://www.uvhci.fr
*******************************************************************************

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: FEBS Course Sofia 2009
From: Rudolf Ladenstein rudolf {- dot -} ladenstein {- at -} KI {- dot -} SE
Date: 2008-12-03

Next message:
Subject: Re: Fwd: site mutation evaluation
From: Juergen Bosch jbosch {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-12-03