Dear Gregg,
Ideally you should not detwin the data for refinement as the
detwinning procedure will degrade your sigmas. Just refine against
twinned data giving the twinning matrix and twin fraction.
Refmac5 does not allow you that (yet) but other software packages do:
SHELX, CNS/X and Phenix.refine (I guess). At 2.1 A I'd use SHELX
(personal taste). Lower than 2.5 A CNS.
Refmac5 as soon as it becomes available.
R.
On 13 Dec 2006, at 21:43, Gregg Crichlow wrote:
Dear CCP4BB:
We have a protein-DNA complex from a twinned crystal (space group
P31). I detwinned the data and refined the structure to 2.1 A with
Rfree=28.8% before adding water and nucleotides. We can only
observe density for two of the 25 nucleotides. I noticed that the
B-factors are very high (around 50-60 A^2). Not many water
molecules can be added using a 80 A^2 cutoff. We determined the
structure of the unbound protein, and the B-factors are almost as
high. I tried fixing the B-factors at 20, but Rfree increased to
30.9%. Is this indicative of an error that can be fixed? Thank you.
Gregg
*******************************************
Gregg Crichlow
Dept. of Pharmacology
Yale University
P.O. Box 208066
New Haven, CT 06520-8066
*******************************************
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Randall Division of Cell and Molecular Biophysics
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