I dont know if you looked at your Wilson plots at 3A and 2.3A - I think
you can see from them how hard it is to estimate a decent overall B
factor at 3A, and how meaningless any estimate will be. The "B factor"
is in fact a fudge factor to get a best fit between your |Fobs| and
|Fcalc| and will reflect the quality and completeness of your low
resolution measurements, how much solvent you have modelled etc etc
rather than the actual temperature factor of the atoms. I would restrain
the Bs tightly to your 2.3A starting set, and not worry..,
Presumably you have solved this structure only to see what the mutation
does and you will deposit the 2.3A one?
Eleanor
fang sheng wrote:
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Hello, All,
I have a 3.0 A data set in space group I41 and got a solution from
MolRep.
When I put it for refinement in refmac under " restrained refinment "
patten, I get 28.7% and 35.5% for R and Rfree, respectively. The
B-factor is only 18.78, unusally low compared to 45.0 ,which is for
2.3 A data from its mutant. I assume a similar B factor between them
since there is one amino acid residue difference out of 500 residues
in total. Am I wrong about it? The worse is refinement only gets
Rfactor drop a little and Rfree increase the same amount.B factor
keeps getting lower and lower. fixing B-factor within the range of 20
-200 doesn't do much good.
The Rmerge in highest resolution shell is kind of high, as 60% while
other factors seem all decent. I though it was fine. But now the low B
factor and high Rfree make me think maybe I should have data
reprocessed for a lower Rmerge. I played with weighting term(
0.05-0.20) and doesn't change things much.Does anyone have the same
experience and please comment on it. Any imput is appreciated.
Regards
Fang Sheng
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