Rerun truncate on your data ans look at the graphs - they often give
clues if the <I> distribution is distorted..
Eleanor
PS - maybe we are a nervous lot, but we always re=process synchroton
data again at home with time to think about it..
James Pauff wrote:
Hello all, thank you for the responses. Just to clear up a couple of things...
1) My dataset was acquired on a synchrotron and scaled/truncated there. To my
knowledge they used the same procedure as for other structures that we have
obtained there...which have had no B factor issues. Granted, our modified
protein is of a different spacegroup than previous.
2) I have not used/touched the TLS parameters at all.
The idea that our 73% completeness (thus lacking 27% of the 'weakest'
reflections) has lead to an artificially low B factor sounds most appealing at
this point?
As usual, I greatly appreciate all of your insights here!
Best,
Jim
--- On Wed, 8/20/08, Eleanor Dodson <[EMAIL PROTECTED]> wrote:
From: Eleanor Dodson <[EMAIL PROTECTED]>
Subject: Re: [ccp4bb] Lower completeness, decent R factors, but low B factor...
To: [EMAIL PROTECTED]
Cc: [email protected]
Date: Wednesday, August 20, 2008, 4:30 AM
James Pauff wrote:
Hello all,
I have a refined structure at 2.6 angstroms that at
about 73% completeness at this resolution. The I/sigma is
about 2.0 at 2.6 angstroms, and the omit density for my
ligands is great contoured at 3.0sigma. My Rcryst is 19 or
so and the Rfree is 24.5 or so.
HOWEVER, my mean B value is 13.9, whereas my other 2
structures (at 2.2 and 2.3 angstroms, same protein, >95%
completeness) have mean B values of 22+. Any suggestions as
to what is going on here? I'm having trouble explaining
this.
Thank you,
Jim
Have you used TLS - listed B factors will then be given
relative to the
TLS parameters. You need to run tLSANL to get a more
realistic value.
Eleanor
But in fact temperature factors are rather harder to
estimate at lower
resolutions than higher. Look at your <Fo> and
<Fc> curves v resolution
( part of a REFMAC loggraph) and you can see that sometimes
the overall
scaling struggles to get a reasonable fit..
