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Re: high B-factors for some ncs copies
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On Fri, 25 Jun 1999, Susan Heffron wrote:
> Chain name Atoms Bave Bsdv Bmin Bmax
> M1A 2894 33.57 18.77 2.00 100.00
> M1B 2894 42.50 19.15 2.00 100.00
> M2A 2894 ** 58.96 ** 24.67 4.87 100.00
> M2B 2894 ** 56.48 ** 25.61 2.00 100.00
> M3A 2894 34.52 21.01 2.00 100.00
> M3B 2894 40.98 21.16 2.00 100.00
> WAT 80 31.76 12.33 5.44 69.18
>
> Two copies of my molecule have alarmingly high average B-factors.
Not really. I've had entire *structures* with that sort of average
B-factor. Interesting, however that even when the <B> is 59 A^2 in one
chain there are some very low B-factors in the structure - is this
reasonable ?
I've seen this behaviour before - the "second" CDK2 molecule in
CDK2:CyclinA had a much higher <B> than the rest of the complex (2
complexes per asymm unit). Doubtless there are many other examples.
> How should I check whether these high B-factors indicate a problem with
> chains m2a and m2b, or whether they simply have high B-factors?
In order of decreasing effort:
1. Look at the density - does it look like it fits ? If so, the <B> is
probably a "real" effect.
2. Do refinement without NCS restraints and compare the molecules - this
may point out if the chain doesn't obey the NCS that well and you're
just forcing it out of place (the B-factors just increase to flatten
out the badly-placed atoms). Compare with/without NCS models.
3. If you are refining individual B-factors, is the increased B-factor a
trend across the whole chain, or is it just in the loop regions (which
are more likely to deviate from NCS) ?
4. Your R-free is 23%, chances are you haven't made any large-scale
errors like assigning the NCS inappropriately.
Phil
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