[phenixbb] strategy of refinement for a structure phased by bromide soaking
pascal at msg.ucsf.edu
Thu Jan 10 16:30:13 PST 2008
I have a 1.8A resolution data set of a protein collected on a crystal
soaked in KBr and I am solving using Phenix.
I used AutoSol and gave a rough estimate of f_prime and
f_double_prime for the Br scatterer as a starting point.
It worked great and Phenix found 31 Bromide ions (only one is fully
occupied) and the resulting map is remarkably clear. Automatic
building has done a great job and I was able to build most of the 4
monomers present in the AU.
However I am confused and have a couple of questions.
1-As Phenix started it generated a
fobs_experimental_phases_free_Rflag.mtz file. I have been using this
file and no longer my data.hkl file for further refinement.
I would like to know why the best_solution after the automatic
building run does not contain any of the Bromide ions. It has water
molecules but no Bromide ions? What is the reason for that?
2-I have been refining against the mtz file I mentioned but without
any of these Bromide ions and although the refinement is converging ,
I suspect I have been doing something bad and wrong.
Should I start my refinement again from the first best pdb after
automatic building and include right away the bromide ions with
simultaneous f_prime, f_double_prime and occupancy refinement for the
As it stands now the Rfree is 22.9 and the Rfac is 19.7. The map
looks fine except for the solvent, some of this atoms are obviously
bromide and there is extra density in the Fo-Fc around some "solvent"
Thanks a lot in advance for your suggestions.
University of California San Francisco
Department of Biochemistry and Biophysics
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