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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: Uppsala University Practical Protein Crystallization Course (U2P2C2)
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-02-08 		Next message:
Subject: Re: an over refined structure
From: Sue Roberts suer {- at -} EMAIL {- dot -} ARIZONA {- dot -} EDU
Date: 2008-02-08


Subject: Re: an over refined structure
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2008-02-08
Dirk Kostrewa wrote:
> Dear Dean and others,
>
> Peter Zwart gave me a similar reply. This is very interesting
> discussion, and I would like to have a somewhat closer look to this to
> maybe make things a little bit clearer (please, excuse the general
> explanations - this might be interesting for beginners as well):
>
> 1). Ccrystallographic symmetry can be applied to the whole crystal and
> results in symmetry-equivalent intensities in reciprocal space. If you
> refine your model in a lower space group, there will be reflections in
> the test-set that are symmetry-equivalent in the higher space group to
> reflections in the working set. If you refine the (symmetry-equivalent)
> copies in your crystal independently, they will diverge due to
> resolution and data quality, and R-work and R-free will diverge to some
> extend due to this. If you force the copies to be identical, the R-work
> & R-free will still be different due to observational errors. In both
> cases, however, the R-free will be very close to the R-work.
>
Ah- that's going way to fast for the beginners, at least one of them!
Can someone explain why the R-free will be very close to the R-work,
preferably in simple concrete terms like Fo, Fc, at sym-related
reflections, and the change in the Fc resulting from a step of refinement?

Ed

CCP4bb navigation

CCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008
Previous message:
Subject: Uppsala University Practical Protein Crystallization Course (U2P2C2)
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-02-08 		Next message:
Subject: Re: an over refined structure
From: Sue Roberts suer {- at -} EMAIL {- dot -} ARIZONA {- dot -} EDU
Date: 2008-02-08


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