Re: [ccp4bb] very high B-factor

[Pavel Afonine]

Hi,


I'm working on a crystal structure with resolution of 2.2A. At the final
> step, I use different strategies to refine the structure, they are:
> no4: strategy=individual_sites+individual_adp+tls / set_b_iso=20
> results: Rwork/free=0.2052/0.2658  b-factor=11.4/136.8/48(min/max/average)
>
> no5: strategy=individual_sites+individual_adp+tls / set_b_iso=10 /
> optimize_xyz/adp_weight=true
> results: Rwork/free=0.2161/0.2639  b-factor=11.3/135.2/48.4(min/
> max/average)
>


make sense to me, both - the strategy and results. Getting the same results
using different starting B is also a good sign.



> no6: strategy=individual_sites+individual_adp / anisotropic for all
> residues and isotropic for water /
>          set_b_iso=10 / optimize_xyz/adp_weight=true
> results: Rwork/free=0.2183/0.2706  b-factor=10.9/144.6/45.7
> (min/max/average)
> PS: the results is read from pdb file
>

This does not make sense: 2.2A isn't good enough to refine all residues
with anisotropic ADP.



> The results showed that the strategy of no5 is the best one.
>


Both, no4 and no5 looks same to me.



> And my questions are:
> 1. Which strategy should I choose to refine my structure? Or any other
> suggestions to refine the structure at 2.2A resolution?
>


Your no4 and no5 look fine. Make sure you let phenix.refine to add water
automatically as part of refinement run. Check manually at the very final
stage.



> 2. Does it possible that some residues have very high B-factor in "B
> factor variance Graphs", while in the pdb file， the b-factor of
> corresponding residues are relatively low? For example, one residue have
> B-factors of 417 in "B factor variance Graphs", but in PDB file the b
> factor is 76. Does the two factor mean the same thing?
>


I don't know how that analysis works. Perhaps it's looking at variance of
local Bs not the absolute value.



> 3. If i want to set the weight manually, which parameter should i set,
> wxc/wxc_scale? or others?
>

wxc_scale for coordinates, wxu_scale for ADP. Normally, though, you are not
expected to do this if you let the program to optimize weights.

Pavel