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: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-12-03

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

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

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
>

CCP4bb navigation

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

Previous message:
Subject: Re: Temperature factor discrepancy
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-12-03

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