Re: [ccp4bb] Temperature factor discrepancy

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

Previous message:
Subject: Re: Temperature factor discrepancy
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-12-03

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

Subject: Re: Temperature factor discrepancy
From: Dirk Kostrewa kostrewa {- at -} LMB {- dot -} UNI-MUENCHEN {- dot -} DE
Date: 2008-12-03

This reminds me of a potential problem with low resolution data that
you might have: if any strong reflection (or a couple of them) is only
partially measured, because it is in the half-shadow of the beamstop,
then the measured intensity is too small, which in turn results in a
too low overall B-factor. For bulk-solvent correction, the Bsol is
then usually at its lower limit and the overall B might still be too
low. An easy way to check this is to re-run TLS, bulk solvent
correction and refinement excluding the lowest resolution shell (say,
use 20, 30, 40 A instead of 50 A or 100 A, or whatever) and check
whether the overall Bs are still too small. If not, you could try to
find out which reflections are the culprits and exclude them.

Good luck,

Dirk.

Am 03.12.2008 um 12:17 schrieb Eleanor Dodson:

> Then I think it is the problem of fitting the TF parameters into low
> resolution data.
> REFMAC tries to use the lowest ( < 9A) data to get the solvent B
> factor and then after applying that correction to get an overall B.
> Many Wilson plot programs only use the data from 4A out, with the
> belief that the lower resolution stuff is so entangled with cell
> content distribution and solvent scattering that it is un-scramble-
> able.
> For higher resolution data sets the two methods usually agree pretty
> well. At low resolution I am not sure which is the better.. Arp/wARP
> tries to be smarter but onerarely uses it at that resolution..
>
> So it is a bit like comparing apples and pears - I doubt if any
> sensible conclusions can be drawn.
> Eleanor
>
> Wim Burmeister wrote:
>> Eleanor Dodson a écrit :
>>> Wim Burmeister wrote:
>>>> 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
>>>>
>>> Are you using TLS? B factors in the pdb are always relativre to
>>> the TLS paramters unless you have run TLSANL
>>> Eleanor
>>>
>>>
>>>
>> Dear Eleanor, there is no TLS used.
>>
>> Yours
>>
>> Wim
>>

*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostrewa@lmb.uni-muenchen.de
*******************************************************

CCP4bb navigation

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

Previous message:
Subject: Re: Temperature factor discrepancy
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-12-03

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