> we are refining several structures from data collected in cryo temperatures
> and have trouble refining the bfactors. We are starting off with the grouped
> B-factor refinement at 2.3-2.5 A resolution. Currently my structure is at
> 2.3 A, with 27671 reflections used for 4620 atoms (560 residues and 179
> waters). The problem is that if I refine the B-factors I end up with lots
> of B-factors of 2.0 (the minimum) and at some places, lower B-factors for
> the main chain than for the side chain portion.
Could there be a problem with the scaling of the data? What value
for overall B-factor do you get from a Wilson plot? How does this
compare to the average B-factor for the whole structure? Do the buried
residues have lower B-factors than surface residues? Do the maps look
good for the low-B residues? What happens to the freeR when you
refine group B's?
Just a few things to consider....