[Protein-crystallography] CNX MR and refinement

Jorge Iulek iulek at interponta.com.br
Fri Jul 21 09:41:06 EST 2006


    Two suggestions:
a) Are you sure the low resolutions were integrated/scaled properly ? what 
are the R-symm's for the low resolution shells ?
b) Try to use TLS tensors within the refmac5 program (try some sensible 
models for rigid groups). I saw several cases in which this lowered much the 
residual indeces, although your problem seems to be more at the low 
resolution shell.
    Of course, the problem could be diverse. But the tywo above might give 
some insight, if not in some cases solve the problem.


"Maxwell" <laobao862 at hotmail.com> wrote in message 
news:1153410721.751001.205840 at p79g2000cwp.googlegroups.com...
> Hi, all,
> I am trying to determine a structure with Molecular replacement. The
> data was collected to 1.7 A in R32 spacegroup with one molecule per
> ASU. CNX found a solution and R factor and R-free started in mid 40s
> and went to 35 and 43 after simulated annealing (with bulk solvent and
> bfactor correction). Anyway, after several rounds of adjustment and
> positional and individual B-factor refinement, the R factor is stuck at
> 27% with R-free of 31%. At this point, I have done anything I could
> think of, but could not lower the R factors anymore. I have included
> all the water molecules I could find. A look at the output of
> positional and b-factor refinement, it seems to me that the R-factors
> for the low resolution range is quite high,  R factor is 37% for 4.69 A
> to 500 A with R-free of 48% for the same resolution range.
> Is this an indication that my MR solution is problematic? Any other
> refinement procedures I could use to lower the R-factors some more?
> Thanks in advance.
> Maxwell Wang, Ph. D.
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