You dont say if your two molecules are in the same orientation with a
translation vector between them ( you need to check the native Patterson
for big off origin peaks - MOLREP does this by default, or use the CCP4i
Molecular replacement task - Analyse data for MR.
If that is the case you may have a data set with many eweak reflections
which can produce a higher than expected R factor..
Eleanor
Michael Hothorn wrote:
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Dear list members,
I am currently trying to refine a structure in primitive orthorhombic
space-group P212121 with the cell dimensions:
46.24 66.63 73.79 90 90 90
tha data process nicely in the primitive orthorhombic setting: Rmeas
overall 0.067 and 0.17 in the highstet shell, 100% completeness and
I/SIGMA 22 and 9 in the highest shell. Based on the systematic absences
along H,0,0 0,K,0 0,0,L, the space-group is P212121 and I found a nice
solution with two molecules in the AU using phaser. Clear difference
density shows the location of two 10-residue sized peptides that I build
in. However, at 2.1 A resolution refinement in either Refmac (including
TLS refinement) or CNS gets stuck at a R/Rfree of 0.27/0.33. The geometry
looks very resonable and I only find two sensible Ramachandran outliers
in the peptide region.
As there is obvioulsy a problem in refinement, I have tried to solve the
structure in either P222, P21212 or P2221 without success. I then
processed the data in P2/P21. The data processing statistics look very
similar to the oP case with a beta angle very close to 90 deg (90.010).
Of course I can also solve the structure in P21 and in P1, however I do
not see a clear improvment in the refinement.
As there is no strong difference density or geometry problems, I am
wondering what might be going on.
Do the cell constants and SG settings allow for any type of twinning? I
had a look at the cumulative intensity distribution in scala without
spotting anything strange. Also, the packing rules out the presence of a
third molecule... What other problems could I test for?
any help/hint/suggestion is highly appreciated
thank you!
michael
Michael Hothorn, Ph.D.
Structural & Computational Biology Unit
European Molecular Biology Laboratory (EMBL)
Meyerhofstrasse 1
69117 Heidelberg
Phone 0049(0)6221 387 268
Fax 0049(0)6221 387 519
http://www.hothorn.de
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