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Re: [ccp4bb] an over refined structure
 

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CCP4bb <-- 2008 <-- February 2008 <-- 04 February 2008
Previous message:
Subject: an over refined structure
From: "George M {- dot -} Sheldrick" gsheldr {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2008-02-04 		Next message:
Subject: Re: an over refined structure
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-02-04


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

Thank you very much for your suggestions. I answered the questions as follows.
I used NCS before rigid body refinement. After that I did not put NCS restraints in the restrained refinement and TLS+restrained refinement because it raised the R/Rfree quite a lot.
The resolution is 2.8 A.
I did not check twinning. I will do that soon.
I used PHASER to solve the structure and the density of the N-domain (~ 50 a.a) in one molecule is not good, with a lot of broken density for the backbone.
I used the TLS in the refinement. I usually used the initial TLS parameters (with only residues in group, no coordinates for the center) for all the TLS refinement. When I used the refined TLS parameters, the refinement would go divergence.
I only added about 120 water molecules for the whole structures.
I will update the information after I try further refinement.

Best wishes,

Sun

Anastassis Perrakis wrote: 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.



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