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CCP4BB  May 2008

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Subject:

Re: Refinement of anisotropic data

From:

Ethan A Merritt <[log in to unmask]>

Reply-To:

Ethan A Merritt <[log in to unmask]>

Date:

Tue, 20 May 2008 22:54:58 -0700

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On Tuesday 20 May 2008 22:24, Pavel Afonine wrote:

I agree with Pavel - it is suspicious that TLS refinement
would increase Rfree.  That really shouldn't happen.

Are your 3 data sets are truly isomorphous, or could it be that the
one with the bad R factors is really in a lower symmetry space group?
What is the mergine Riso between data sets?

	Ethan



> Hi Yang Li,
> 
> - the data-to-parameters ratio is not good for individual anisotropic 
> ADP refinement at this resolution;
> - I'm wondering why TLS refinement increases the Rfree... How did you 
> select the TLS groups? Did you try to use TLSMD for this (thanks Ethan, 
> it produces TLS groups selections ready to use in phenix.refine);
> - is there any NCS? if so, use it.
> 
> You can also try to use this server to correct for data anisotropy:
> http://www.doe-mbi.ucla.edu/~sawaya/anisoscale/
> 
> Cheers,
> Pavel.
> 
> 
> On 5/20/2008 10:00 PM, yang li wrote:
> > Hi,
> >     I have a structure with 3 different resolutions, 2.3A, 2.4A, 2.5A, 
> > the qualities seem normal, not good but also not too bad.
> > The B factors along a,b,c axis have notable difference, for example 
> > B(a)=80, B(b)=30, B(c)=20. We used molecular
> > replacement to solve the structure. For the 2.3A data, the final Rfree 
> > is 0.265 from phenix.refine without tls since tls will
> > increase the Rfree much. But for the 2.4A data, the Rfree wonnot low 
> > down to 0.32, though the map seems not bad(with
> > only a few solvent atoms). And for the 2.5A data the Rfree is even 
> > higher than 0.4. For all of them I used thinshell and 
> > followed the same procedure:
> > MR-->rigid body refinement-->restrain 
> > refinement-->phenix.autobuild-->manually check-->phenix.refine(ordered 
> > solvent)
> > And autobuild can always build more than 80% residues with mostly side 
> > chains.   
> >     This is not a big structure with no more than 1000 residues in 2 
> > molecules. I wonder why the R values keep so high.
> > Do I need to run anisotropic refinement for such resolutions? Or any 
> > other reasons?
> >  
> >  
> > Thanks!
> >  
> 

-- 
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

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