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Re: [ccp4bb] Differences in R and Rfree
 

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CCP4bb <-- 2007 <-- March 2007 <-- 09 March 2007
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Subject: Differences in R and Rfree
From: Nicholas Noinaj noinaj {- at -} UKY {- dot -} EDU
Date: 2007-03-09 		Next message:
Subject: Re: Removal of bacterial Hsp70 contaminant from recombinant protein
From: Dr shekhar shekhar {- at -} CDFD {- dot -} ORG {- dot -} IN
Date: 2007-03-09


Subject: Re: Differences in R and Rfree
From: HKim {- at -} DECODE {- dot -} COM HKim {- at -} DECODE {- dot -} COM
Date: 2007-03-09
Hi, Nick,

An R-factor of 0.16 seems low for a model refined against 2.4 A data. What
are you using for the MATRIX weight in REFMAC? Here's a guide for
selecting a proper MATRIX weight
http://www.dl.ac.uk/list-archive-public/ccp4bb/2005-10/msg00592.html For
refinement against a 2.4 A data set, I usually use a MATRIX weight of 0.1.
CNS automatically determines a proper weighting, which is probably why
the spreads between your residuals with CNS refinement look more
reasonable. I would also use a 5% R-free set. When I started reading
your post, my first thought was that your Ramachandran plot must look like
a blast of buckshot. But if the stereochemistry looks good by PROCHECK, I
don't think there's anything fundamentally wrong with your methods. Good
luck,



Hidong










Nicholas Noinaj
Sent by: CCP4 bulletin board
03/09/2007 06:22 PM
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Subject
[ccp4bb] Differences in R and Rfree






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
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