[phenixbb] Diffraction anisotropy
Pavel Afonine
pafonine at lbl.gov
Thu May 5 17:28:29 PDT 2011
Hi Ina,
> I am refining a structure of 2.3A resolution. The R values with and
> without bulk solvent and anisotropic scale are quite different as you
> can see here:
>
> Start R-work = 0.3751, R-free = 0.5562 (no bulk solvent and
> anisotropic scale)
> Final R-work = 0.3741, R-free = 0.5557 (no bulk solvent and
> anisotropic scale)
>
> Start R-work = 0.2298, R-free = 0.2974
> Final R-work = 0.2261, R-free = 0.2970
the values reported with "(no bulk solvent and anisotropic scale)"
correspond to the R-factor values calculated using
Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s2/4) *
Fmask)
where AnisoScale = k_sol = b_sol = 0, which means "no bulk solvent and
anisotropic scale".
given a typical solvent content of macromolecular crystals ~50% and
always some anisotropy, the values do not look too surprising to me.
Actually, the R-factors before bulk-solvent correction and scaling are
rather confusing (although may be useful in some cases) so phenix.refine
does not output them anymore at the very bottom of .log file (you can
still find them somewhere in the log file).
Pavel.
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