[ccp4bb] low-res cutoff in refinement

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CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008

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From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
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Subject: Re: low-res cutoff in refinement
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2008-01-24

Subject: low-res cutoff in refinement
From: "Van Den Berg, Bert" Lambertus {- dot -} VandenBerg {- at -} UMASSMED {- dot -} EDU
Date: 2008-01-24

Hi all,

during refinement of our (membrane protein) structures, basically in all cases the R/Rfree values depend a lot on the low resolution cutoff. Putting the cutoff at lower res (20-50 A) results in substantially higher R/Rfree values (sometimes few percent). For this reason we mostly refine the data from the high-res limit down to 10A or so. I have noticed that this occurs fairly often in the literature, but I don't know if this is a membrane protein related issue or not.

Could it be that the bulk solvent model used in CNS (we refine exclusively with CNS) does not model the situation with membrane proteins, due to the presence of detergents? Or is it related to data collection issues (low-res spots overloaded etc)? Anything else? What could be done to overcome the problem, and to use all the data in refinement?

Thanks, Bert

Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Biotech II, 373 Plantation Street, Suite 115

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008

Previous message:
Subject: Re: Real space rotation translation
From: Edward Berry eaberry {- at -} LBL {- dot -} GOV
Date: 2008-01-24

Next message:
Subject: Re: low-res cutoff in refinement
From: Pavel Afonine PAfonine {- at -} LBL {- dot -} GOV
Date: 2008-01-24