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[ccp4bb] Differences in R and Rfree
 

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CCP4bb <-- 2007 <-- March 2007 <-- 09 March 2007
Previous message:
Subject: Re: High overall b-factor
From: ezra peisach epeisach {- at -} MED-XTAL {- dot -} BU {- dot -} EDU
Date: 2007-03-09 		Next message:
Subject: Re: Differences in R and Rfree
From: HKim {- at -} DECODE {- dot -} COM HKim {- at -} DECODE {- dot -} COM
Date: 2007-03-09


Subject: Differences in R and Rfree
From: Nicholas Noinaj noinaj {- at -} UKY {- dot -} EDU
Date: 2007-03-09
Hi,

I am working on a 2.4 angstrom structure that is in its final stages of refinement and finding that REFMAC5 is giving a large difference between R and Rfree (10%), 0.16 and 0.29, respectively. 2Fo-Fc maps looks great and there is very little density in the difference maps. My model covers the entire protein sequence, except for ~5 residues on N-term and 3 residues on C-term. I then used the model for refinement (annealing) within CNS, and found that R and Rfree are relatively similar, 0.2 and 0.28, but in better agreement.

I have read other posts addressing similar questions, but still unsure what my problem could be, if there is one. While I don't mind repeating things in CNS, I would really like to learn to be completely reliable on CCP4 Suite as much as possible, since i really like the REFMAC5 - Coot duo. I would appreciate any suggestions or comments you might offer. Given how nice the density maps look and that the model passes procheck analysis with very few suggestions for further investigations, i am unsure when to go from here.

Thanks in advance for all feedback!




Cheers,
Nick

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 09 March 2007
Previous message:
Subject: Re: High overall b-factor
From: ezra peisach epeisach {- at -} MED-XTAL {- dot -} BU {- dot -} EDU
Date: 2007-03-09 		Next message:
Subject: Re: Differences in R and Rfree
From: HKim {- at -} DECODE {- dot -} COM HKim {- at -} DECODE {- dot -} COM
Date: 2007-03-09


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