My experience with structures derived from data of similar resolution
limits (3,7A, 4.2A) is that B-factors fall in a range similar to 100-280A.
Such spread was preserved even when the model improved and R-free was
reduced to mid-twenties. Without B-factor refinement R-free was much
larger. Your R-factor is rather close to R-free for such a low resolution
data refined with B-factors; it may have happened due to a "fortuitous"
choice of the R-free set, if so, the quality of the structure would be
somewhat lower than indicated by R-free.
Zbyszek
Re: "fortuitous"
Random fluctuations inherent to the definition of R-free set may generate
quite significant range of values. If the choice of R-free set generates a
lower value, this may be fortuitous in terms of the structure being
subject to review in a publication; but it does not make that structure
any more accurate.
> Dear All,
> I am facing troubles in refining structure (C2221 space group) at 4A
> resolution . The current Rwork/Rfree stalls at 35.8/37.7.Given low
> resolution, the total number of unique reflections accounts to *19356
> while
> number of atoms in pdb corresponds to **3893. *At this very low
> resolution,
> the number of available observations are insufficient to support the
> refinement of four parameters (x, y Z, Biso) and therefore i think the
> modeled atomic displacement (B-factors) are excessively high ranging from
> 100-280 which is scary at this moment.
>
> Is there any illustrative parameters to work on which might be useful for
> putting control over the shooting up of B-factors during refinement. I
> tried incorporating the group B-factor refinement with TLS group but seems
> like is not much useful.
>
> I would appreciate any incoming suggestions and thoughts on adopting
> crucial refinement strategies pertaining to this resolution.
>
> Thank you
> Appu
>
Zbyszek Otwinowski
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-8816
Tel. 214-645-6385
Fax. 214-645-6353
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