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Re: [ccp4bb] an over refined structure
 

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CCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008
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Subject: Re: an over refined structure
From: Ronald E Stenkamp stenkamp {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-02-08 		Next message:
Subject: FW: Different chains in the dimer
From: "Skrzypczak-Jankun, Ewa" Ewa {- dot -} Skrzypczak-Jankun {- at -} UTOLEDO {- dot -} EDU
Date: 2008-02-08


Subject: Re: an over refined structure
From: Axel Brunger brunger {- at -} STANFORD {- dot -} EDU
Date: 2008-02-08
In such cases, we always define the test set first in the high-symmetry
space group choice. Then, if it is warranted to lower the
crystallographic
symmetry and replace with NCS symmetry, we expand the test set
to the lower symmetry space group. In other words, the test set itself
will be invariant upon applying any of the crystallographic or NCS
operators,
so will be maximally "free" in these cases. It is then also possible
to
directly compare the free R between the high and low crystallographic
space group choices.

Our recent Neuroligin structure is such an example (Arac et al.,
Neuron 56, 992-, 2007).


Axel




On Feb 8, 2008, at 10:48 AM, Ronald E Stenkamp wrote:

> I've looked at about 10 cases where structures have been refined in
> lower
> symmetry space groups. When you make the NCS operators into
> crystallographic
> operators, you don't change the refinement much, at least in terms of
> structural changes. That's the case whether NCS restraints have
> been applied
> or not. In the cases I've re-done, changing the refinement program
> and dealing
> with test set choices makes some difference in the R and Rfree
> values. One
> effect of changing the space group is whether you realize the copies
> of the
> molecule in the lower symmetry asymmetric unit are "identical" or
> not. (Where
> "identical" means crystallographically identical, i.e., in the same
> packing
> environments, subject to all the caveats about accuracy, precision,
> thermal
> motion, etc). Another effect of going to higher symmetry space
> groups of
> course has to do with explaining the experimental data with simpler
> and smaller
> mathematical models (Occam's razor or the Principle of Parsimony).
>
> Ron
>

Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University

Web: http://atb.slac.stanford.edu
Email: brunger@stanford.edu
Phone: +1 650-736-1031
Fax: +1 650-745-1463




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CCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008
Previous message:
Subject: Re: an over refined structure
From: Ronald E Stenkamp stenkamp {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-02-08 		Next message:
Subject: FW: Different chains in the dimer
From: "Skrzypczak-Jankun, Ewa" Ewa {- dot -} Skrzypczak-Jankun {- at -} UTOLEDO {- dot -} EDU
Date: 2008-02-08


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