Preamble:
I have an interesting crystal form with 3 monomers (~400aa) at full
occupancy and apparently one at much reduced occupancy. It was built
recently from Se-SAD and was in moderately good condition: Rfree=32% for
trimer, 2.6 Å. In recent refinement cycles it became obvious that there
was a 4th monomer in a region of weaker/choppy 2Fo-Fc and Fo-Fc density
that corresponded to a "confusing" set of low-occupancy SeMet sites
found by SHELXD and Phaser-EP. The experimental map was bad in that
region and was probably flattened during density modification anyway, in
retrospect.
Question:
Phaser failed to find the 4th monomer after trivially finding the other
3 with a recent version of the monomer. I'm wondering if there's a way
to indicate "this one is partial occupancy" to Phaser, or if there's a
way to improve the odds of success beyond just lowering the expected %
homology. Or if anyone has had success with other programs. This is
perhaps a rare edge case but I naively expected Phaser to work.
In the end I used the weak SeMet sites to locate the monomer and the
occupancy appears to be around 0.32 in refinement.
Cheers,
Phil Jeffrey
Princeton
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