On 21 May 2008, at 7:00, 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?
Likely twining. Run phenix.xtriage and read carefully the output for
any signs of it,
then refine the twin fraction in twin.refine (if applicable)
We have a series of about 8 structures of the same protein, 5 are
fine, 3 are twinned.
Same pathology as you observe,
Tassos
Thanks!
