[phenixbb] R factor with no bulk solvent and anisotropic scale

Alexandre Urzhumtsev sacha at igbmc.fr
Thu May 6 23:58:28 PDT 2010

Dear Shunsuke,

you indicated at the first line of you mail that you are working at a low 

>I am refining a low resolution data (4.1 A).

where the bulk solvent contribution is essential ; at lower resolutions it 
becomes even dominant.

>Start R-work = 0.3762, R-free = 0.4043 (no bulk solvent and anisotropic scale)
>Final R-work = 0.5019, R-free = 0.5204 (no bulk solvent and anisotropic scale)
>Start R-work = 0.2665, R-free = 0.3195
>Final R-work = 0.2578, R-free = 0.3126

Therefore it is normal that ignoring this component gives you a model with 
a very high R. So the real question is to be sure that the bulk solvent 
parameters have correct values (you did not give them). Looking at your 
total R-factors, I would believe it is OK. The R-factors perfectly 
correspond to the linear approximations  :

         R       = 0.091 ln(d) + 0.134   = 0.262 (you have 0.258)
         Rfree-R = 0.024 ln(d) + 0.020   = 0.054 (you have 0.055)

(see Urzhumtsev, Afonine, Adams, 2009, Acta Cryst D65, 1283-1291)

Best regards,


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