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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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