sigma_cutoff

[Matthew Meyer]

    I've been re-refining some mutant structures.  This time I'm
throwing away peaks where I/sigI < 2.0.  R and Rfree are much improved
(by typically 4 %) over the previous refinements when sigma_cut = 0.0.
However, after expansion to full resolution, far fewer waters are picked
before further picking pushes R back up. I notice that many waters in
the old model are not within hydrogen-bonding distance of anything.  I
recently read that was bad in an article by Kleywegt
(http://journals.iucr.org/d/issues/2000/03/00/gr0949/gr0949bdy.html#BB100).
My question is which is right? Would the reporting of only 3 waters in a
~140 aa protein refined to 2.45 A be an indication for refinement
errors?

--
Matthew G. Meyer
154 S. Frear / 6 Althouse
Penn State University
mgm10 at psu.edu


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