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 <[log in to unmask]> wrote:
> From: Eleanor Dodson <[log in to unmask]>
> Subject: Re: [ccp4bb] Lower completeness, decent R factors, but low B factor...
> To: [log in to unmask]
> Cc: [log in to unmask]
> 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..
