[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) * 

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).


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