Re: [ccp4bb] Low resolution refinement
One more thing though: have you refined with the NCS restraints off or on? Presumably on, seeing that you have a small gap between R and Rfree? It may be worth turning the restraints off or modify the NCS selections: if your 3 molecules are substantially different, applying NCS may make things worse rather than better (ie you’re averaging things that are different).
Good luck, Bert
On 5/19/11 9:02 AM, "Joane Kathelen Rustiguel" <[log in to unmask]">[log in to unmask]> wrote:
Dear all
I am refining a structure at 3.4 A resolution that contains 3 molecules in the
a.u. The chain A sits on a 2-fold crystallographic axis forming the dimeric
functional structure expected for this class of proteins. The other two chains
B and C, which also form the functional dimer, seem to be, somehow, a lot more
flexible than chain A. As a result, whereas the electron density map, b-factor
and geometry for chain A is pretty reasonable for a 3.4 A resolution
structure, the refinement for the other two chains (B and C) does not behave
well. Even playing with different weights for geometry, analysing different
levels of 2Fo-Fc/Fo-Fc maps, using NCS, TLS, etc..., nothing works. The map
for the helical regions is ok, but the electron density map for strands and
loops of chains B and C are broken along the main chain, B-factors are really
high, and the geometry keeps being distorted.
Right now, the R-factor and R-free are 24.2 and 28.6, respectively.
Any suggestions in how to proceed the refinement?
And even a more difficult question, how do we report this type of structure?
How do we deposit those coordinates? We can certainly use chain A as a model
to perform interesting studies of structure-function relationship, but we know
that chain B and chain C have problems.
Any help will be greatly appreciated.
Regards
Joane
--
Joane Kathelen Rustiguel Bonalumi
Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP
Laboratório de Cristalografia de Proteínas
Departamento de Física e Química
Fone: +55.16.3602.4193
