[ccp4bb] Differences in R and Rfree

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

- Programs for crystallography
- X-ray detectors

Basic tutorials:

   - Chemistry
   - Protein
   - Peptide
   - Amino Acids

Xtal community:

- CCP4BB

CCP4bb navigation

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

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

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