Well - some things to consider.
1) Rfree will often go up a bit but this seems too much.
2) Does the mz file have the right spacegroup in the header?
It is possible to have processed data in one spacegroup and have the Se
solution in the enantiomorph..
You might have to actually CHANGE the spacegroup in the mtz
I use this script to do that
mtzutils hklin1 now.mtz hklout corrected.mtz
SYMM corrrect_SG
end
Eleanor
Vlad Smith wrote:
Hi all,
I have run into an unusual problem and am looking for some help. I am
working with a small protein that is 76 amino acids in length. I have
collected anomalous data and have located the 4/5 selenomethionine sites
using SHELX C/D and SHARP. The map that is produced from SHARP after dm is
pretty nice. I can see secondary structure and side chains. I have
submitted this map to PHENIX autobuild, and it was able to place about 85%
of the model. I have extended the model to be 90% complete. Upon
inspection of the model, the selenomethioine locations match both the
sequence and the peaks in the anomalous difference fourier map. I was
surprised to find that the model actually falls into 2 ASUs. When I start
my refinement using phenix.refine and/or refmac, the R-factors start off in
the mid .40s, but after a round of simulated annealing the R-free rises to
the mid .50s. I can go back and remove a section of the model, run a round
of refinement, and have the density return for that section of the map,
which I interpret as the phases being some what correct. Does anyone have
any ideas on what would cause the R-free to be so high? Again, I emphasize
that the experimental map was of rather good quality.
Thanks for your help,
Vlad
