[phenixbb] Problem in reducing R-factor

Pavel Afonine pafonine at lbl.gov
Fri Oct 11 12:17:08 PDT 2013

I'm *thinking* (not doing it right now) to make phenix.refine do 
something of this sort  automatically if the resolution is really 1.3A 
(and not in fact say 1.5 or so but data file has a couple of reflections 
nearing 1.3A, which would tend people claim it is 1.3A resolution!) and 
r-factors are not too far to expected ones given *actual* data 
resolution. Of course "1.3A" in this case is going to be a range between 
1 and 1.5A in terms of data quality.


On 10/11/13 8:39 AM, Nathaniel Echols wrote:
> What happens if you try refining protein atoms (but not waters) with
> individual anisotropic B-factors instead of TLS?  It isn't guaranteed to
> work at 1.3Å, but it usually does (in my hands, anyway).
> Also make sure you have explicit hydrogens added; this will have a
> significant effect at this resolution.  And turn on the water update if
> you haven't already.
> On Fri, Oct 11, 2013 at 6:19 AM, Singh, Bishal
> <b.singh at dkfz-heidelberg.de <mailto:b.singh at dkfz-heidelberg.de>> wrote:
>     Hi all,
>       I am solving a crystal structure at 1.3Å. Completeness of the
>     data-set and Figure of merit at this resolution are 99.5% and 0.62
>     respectively. Structure has two molecules per asymmetric unit. I
>     used TLS parameters and NCS restraints. WXC_scale and WXU_scale are
>     0.50 and 1.0 respectively. Rwork and Rfree are 18.09 and 19.62
>     respectively. I tried with reducing WXC_scale and WXU scale to 0.25
>     and 0.30 respectively but it did not help. Please suggest me if I
>     need to change some parameters. I shall be grateful for your help.
>     Thanking you,
>     Bishal Singh
>     Graduate student
>     University of Heidelberg, Germany
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://phenix-online.org/mailman/listinfo/phenixbb
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list