About B factor refinement

Aaron Oakley s_aarono at EDUSERV.ITS.UNIMELB.EDU.AU
Mon Apr 15 23:10:39 EST 1996


>I want to know how to correctly use them in structure refinements,
>especially the different applying cases of Grouped and Individual.
>Could you please help me on this point?  I am refining an enzyme-inhibitor
>complex structure. The R value has gone down to 23.7%.
>Can I add water moleculesand proceed to refine B-factors now?
>      Thanks!
> 

The type of B-factor refinement you can do will depend on the resolution
of the data. Up to about 2.5A you can do individual B-factor refinement.
from 2.5 to 3.5A you can do grouped B-factor refinement.

The number of water molecules you add will depend on resolution, too.
At low resolution, you won't see any. At high resolution, you will
see many.

B-factor refinement and the addition of water molecules increases
the number of parameters being refined, which may lead to overfitting.
Use freeR to see if this is the case. (see chapter 15 of the Xplor
3.1 manual)

Hope this helps,

Aaron



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