Re: [ccp4bb] coupling between occupancy and b-values in refinement

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

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From: Stuart McNicholas mcnicholas {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-06-01

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From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-06-01

Subject: Re: coupling between occupancy and b-values in refinement
From: mb1pja P {- dot -} Artymiuk {- at -} SHEFFIELD {- dot -} AC {- dot -} UK
Date: 2009-06-01

Dear Patrick

Long ago we (Cheetham et a (1992) J Molec Biol 224:613-628) did some
refinements on hen lysozyme + substrate complexes at 1.75A and 2A
resolution and showed that B and occupancy are negatively correlated,
especially at 2.0A. In simplistic terms this is because at medium
resolution low density at the atomic position could be the result of
either low occupancy or high B factor. We ran parallel refinements
using assumed occupancies at 0.1 intervals. We looked at R factors but
they werent much help - this was pre-Rfree so the latter might be a
valuable criterion now.

I think a good strategy is to refine your substrate complex at
intervals of o=0.1, 0.2 ... (with a non-complex model at 1-o, ass
positions of side chains and waters may well be different) and look at
the B factors. At the correct(ish) occupancy substrate Bs will be
expected to be similar to those of the ligating residues from the
protein. But it does get to be quite subjective until you have higher
resolution.

best wishes
Pete

On 31 May 2009, at 16:58, Patrick Loll wrote:

> Hi all,
>
> I'm looking for a reference to bolster my response to a referee, in
> which I defend my decision not to refine the occupancy of a ligand
> in structure refined at around 2 A resolution (note the ligand
> binding slte lies on a two-fold crystallographic axis, so the
> maximum occupancy is 0.5)
>
> I recall reading a paper a LONG time ago (decades) in which someone
> described some careful refinement experiments, and concluded that
> the correlation between occupancy and B-value is so strong that it
> simply makes no sense to "independently" refine both parameters (at
> least for light atoms, and in the absence of super high resolution
> data).
>
> Alas, all that I recall is this take-home message. I have no idea of
> where the paper appeared, or the names of the authors (or indeed, if
> I'm even remembering the paper's message correctly). I've tried
> trolling through Acta, without success. Does anyone have a better
> idea of where I might find this paper, or one espousing a similar
> message?
>
> Thanks,
>
> Pat
>
>
> -------------------------------------------------------------------------------------
> Patrick J. Loll, Ph. D.
> Professor of Biochemistry & Molecular Biology
> Director, Biochemistry Graduate Program
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St., Mailstop 497
> Philadelphia, PA 19102-1192 USA
>
> (215) 762-7706
> pat.loll@drexel.edu
>
>
>
>

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

Previous message:
Subject: Re: 3D LCD and glasses
From: Stuart McNicholas mcnicholas {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-06-01

Next message:
Subject: Postdoc ad: PX at SGC (U of Oxford)
From: Frank von Delft frank {- dot -} vondelft {- at -} SGC {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-06-01