What is the reason for lower completeness is important.
1) rotation range is not wide enough----you lost frames? What about
the completeness against
resolution shell?
2) too many rejections?
a) symmetry error
b) really bad crystal (this seems not the case)
c) too many overlaps during collection, mosaicity ....
Guess 1) is your case, if I can.
Also, good R factors from low-completeness (either reason above) is
less reliable.
Good luck.
Lijun
On Aug 20, 2008, at 9:24 AM, 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: CCP4BB@jiscmail.ac.uk
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..
Lijun Liu, PhD
Institute of Molecular Biology
HHMI & Department of Physics
University of Oregon
Eugene, OR 97403
541-346-4080
