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Hi,
I have a couple of questions during model refinement. Hopefully
someone could help me.
My crystal diffracted to 2.4Å resolution with molecular weight 40KD.
The crystal belongs to P212121 space group with unit cell dimension
a=72Å, b=73Å, c=88Å. The crystal is not twinned. After molecular
replacement in the resolution range 20-4Å, I got a very good peak for
later CNS refinement.
In rigid body refinement, I am not sure which resolution range I
should use, 20-4Å or 20-2.4Å? I tried both. If I use 20-4Å data,
R=0.3355, Rfree=0.3265. If I use 20-2.4Å data, R=0.3304,
Rfree=0.3207. After 20-4Å rigid body refinement, I also do phase
extension gradually from 4Å to 2.4Å (that is, rigid body refinement
20-4.0Å, then 3.5Å, then 3.2Å, ...until 2.4Å), the result is
R=0.3360, Rfree=0.3268. From the results of R and Rfree, I believe I
should use 20-2.4Å in rigid body refinement. However, I was told to
use 20-4.0Å first, then do phase extension like I said above. Could
anyone tell me why?
The second question is after final refinement and model building, my
R=0.2133, Rfree=0.2333. It looks good. Then I validate the model by
some other programs, like procheck, what If, and MolProbity. After a
painstaking work, I am frustrated to find that my R=0.2056,
Rfree=0.2398. I am confused why after rotamer correction,
Ramachandran check, water check, collision check, etc., my Rfree
increased, not decrease?!
Your help is greatly appreciated!
