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There has been a "stuck refinement" discussion going on over the ccp4bb
for the past few days.
Your unit cell values make me think you might not have twinning.
Twinning in P.O. s.g. is not very common except when two unit cell
lengths are very similar. Folks correct me if I am fibbing here.
If you haven't seen the discussion yet, you are probably going to hear
the foll:
1. look for sharp increase in rfac/rfree with resolution
2. so your data truncated at resolution where the i/sig is 9?? how about
data beyond/higher than 2.1 Ang resolution?
3. not clear from your email if you have already have added waters, ions
etc. if not, this might help
4. how much of protein is accounted for in the model? are there regions
with terrible bfactors?
5. i do not know if "optimize wa" to optimize the x-ray term is a
helpful suggestion for your case. say what, others?
Sorry for this laundry list. Good luck.
Raji
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
