Re: [ccp4bb] an over refined structure

- Protein crystallography

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

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Subject: Re: an over refined structure
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-02-04

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Subject: Re: an over refined structure
From: price {- at -} UCHICAGO {- dot -} EDU price {- at -} UCHICAGO {- dot -} EDU
Date: 2008-02-04

Subject: Re: an over refined structure
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-02-04

Hi -

I don't think there is something necessarily wrong with the values
you report.

A few questions to see *if* something is wrong are:

- as you wrote to Tim you have NCS: do you use NCS restraints ?
- what is the resolution / B factor of the data ?
- have the data been checked for twining ? (phenix.xtriage)
- is the N-term domain of one copy really invisible (then indeed do
remove ...!)
- has TLS been used ?
- did you add waters ? (too many?)

I guess then we can make better suggestions if something is wrong and
if so how its best to fix.

A.

> > I refined a structure with Refmac in CCP4i and the R/Rfree is
> 0.215/0.277. The difference between R and Rfree is too much even
> though I used 0.01 for weighting term in the refinement (the
> default value is 0.3). The RMSD for bond length and bond angle is
> 0.016 A and 1.7 degree.

CCP4bb navigation

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

Previous message:
Subject: Re: an over refined structure
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-02-04

Next message:
Subject: Re: an over refined structure
From: price {- at -} UCHICAGO {- dot -} EDU price {- at -} UCHICAGO {- dot -} EDU
Date: 2008-02-04