[phenixbb] advice for refinement with anomalous information

vincent Chaptal vchaptal at mednet.ucla.edu
Wed Aug 11 17:56:24 PDT 2010


the refinement of my structure brings me to a new point where I would
appreciate any input.
- I solved the structure by molecular replacement.
- The refinement looked good, I was almost ready to deposit but there
always was a fairly big blob of density that i couldn't explain, loosely
coordinated to the protein and far from the active site.

To try to identify what it could be, i calculated an anomalous
difference map (data collected at 1A) and I see a peak right in the
middle of this density.
I have BaCl2 in my crystallization solution so it is the likely guilty
ion! (and with further look, it looks like a loose metal site)

So now, I want to refine with Barium in the density and I was wondering
what was the best way to do it, and since there is anomalous signal, why
not use it?
* I updated to the new version of phenix and it reads I+ and I- (while
the previous version didn't) but under the refinement settings, the
target function ML-SAD is still for developers only. Is it a good idea
to use the anomalous Is for refinement, or:
* should I re-run Phaser-EP to have phases to use in phenix.refine, or:
* should I not bother, the signal is weak anyway (1 barium/ ~400
residues) and continue with my non-anomalous scaled dataset and use the
anomalous signal only for a figure to explain why I put the metal here.

(resolution of 3.4A, quite anisotropic)

I can also try everything but I'd like to understand what would be best.
Thanks very much for your help


Vincent Chaptal

Dept. of Physiology at UCLA


Phone: 1-310-206-1399

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