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 <[EMAIL PROTECTED]> 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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