Re: R-factors and B-factors

[Eleanor Dodson <ccp4@yorvic.york.ac.uk>]

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On Oct 26, 11:02am, alex jack wrote:
> Subject: R-factors and B-factors
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> Dear All:
>
> Could somebody help me answer these questions:
>
> 1. What's generally the acceptable R-factors for a structure, with the
> data of 2.5 A; 3.0 A; and 3.5 A.

  It is better to consider FreeR values - they are (slightly) more reliable..

 Depends on quality of data, and model.
Impossible to generalise.
  R factors > 50% at any resolution probably random.

  Rfactors < 20% for all data at 2.5A probably OK
At lower resolutions ( 3, 3.5A) you can change Rfactor drastically by using
different overall scaling protocols.
Best test of model quality is to look at maps - harder to quantify though!
....
>
> 2. Is it true, that the higher resolution your data has, the lower
> R-factors you should get? Or just the way around?
>

 See above - depends on quality of model, and data..
 Usually model will be better, and Rfactor in comparable shells will go down..
Overall R factors cannot be predicted.

> 3. What's the significance of the atomic B-factors when you have a low
> resolution data, for example, 3.0 A; or 3.5 A.
>


 Very very little - common sense indicates that if the data peters out at that
resolution the overall B must be 50 or greater..
But depending on scaling procedure it can be seriously under-estimated - there
are several structures in the PDB with swathes of negative Bfactors!

Most unlikely..
 Eleanor Dodson

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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
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