I would agree on both points- as to the NCS, there was a very useful study by
Kleywegt
of deposited structures that that released NCS at resolutions that didn't
justify it-
maybe
G J Kleywegt, "Use of non-crystallographic symmetry in protein structure refinement", Acta
Crystallographica, D52, 842-857 (1996).
or
G J Kleywegt & T A Jones, "Where freedom is given, liberties are taken", Structure, 3,
535-540 (1995).
As to outliers, I understand adding (riding) hydrogens can improve the
Ramachandran,
but like enforcing dihedrals this somewhat invalidates the use of the
Ramachandran,
since it's mainly the clashes between hydrogens that define the ramachandran
permitted area. I would not recommend adding H's at this resolution.
If the outlier is well defined in the density, it is probably a real outlier;
If as you say poorly defined, the data is not strong enough to determine the
rotamer so it drifts out, and the rama plot is correctly indicating this.
Ed
Thomas Womack wrote:
On 27 Aug 2010, at 10:55, Petr Kolenko wrote:
Dear crystallographers,
I have a structure at 3.3A resolution, 16 identical chains in AU, merohedral
twinning present. I started to refine using NCS restraints with chain A as a
reference chain. Current Rwork/Rfree is 21/25. There is almost nothing to
refine manually in whole structure now. But, refinement without NCS restraints
results in Rwork/Rfree of about 17/28. What should I do? Or is it possible to
deposit the structure refined using NCS restraints in final refinement?
This seems like a really well-done NCS refinement; using the multi-fold NCS is
allowing you to get what is an excellent Rfree and Rwork-Rfree gap for 3.3A
data. Definitely deposit the NCS-restrained version; refining without NCS
restraints just increases the number of parameters by a factor sixteen and
spends most of those on fitting noise.
1% Ramachandran outliers at 3.3A also seems entirely reasonable.
Tom
