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Summary: B-Factors and Wilson Plot
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Thanks to everyone who responded. The general consensus was that I have
nothing to worry about. Several people pointed out that most
temperature factors for protein structures are underestimated leading to
the bias that
"good" structures should have average temperature factors in the 20-30
A couple of people asked about the solvent content of the crystal. As
some of you guessed, this is high. I have a Vm of 4.0 yielding
an approximate solvent content of 69 %. This explains some of
the thermal motion. It was also suggested to check the native as
well as the SeMet data. The Wilson B values are high for all data sets
that I have, however the native is the lowest.
I was also advised to examine the Wilson plot to look for
typical features of the dip around 5.5 A and the peak around
4 A. In this respect, my Wilson plot looks fine. One last suggestion
to compare the results to refinement with another program. I will
give this a try.
A selection of a few comments I received:
Manfred Weiss wrote:
> as far as I can tell from your post your data seem to be alright.
> A B of 56 is quite high but your data extend to 2.4 A resolution
> only, so that is consistent. A model B being slightly higher
> than that is also ok, since your model is still incomplete.
> The only thing you need to watch is whether your model B keeps
> increasing from one round of REFMAC refinement to the next.
> If it does you should set the overall value back to the 56
> before a new round.
Eleanor Dodson wrote:
> I believe that average B factors given for structures are more often
> too low than too high.. If the data peters out at 3A it is very
> difficult to get any sensible estimate of a Wilson plot gradient, but
> is most likely that a true Av_B should be in the range 80-100, rather
> than 10 as is sometimes given!
> REFMAC values should reflect the gradient of the Wilson plot, and they
> do seem to do so quite well in your case.
Yu Wai Chen sent statistics from a recently solved structure which
were virtually identical to the data I posted.
Hans Raaijmakers wrote:
> Seems fine to me,
> the low B factors (~20) were normal when people only worked on
> crystals that diffracted strongly on weak x-ray sources.
> Synchrotrons and mirror optics allow the measurement of weaker
> diffracting crystals (with higher B-factors).
> I found that different crystals within one batch might yield
> quite different B-factors. (45-75 avg) But they didn't really make any
> difference to the biological interpretation.
Andrew M. Gulick PH 608-262-0529
University of Wisconsin
1710 University Ave. Madison WI 53705