If I go back to my SCALA mtz and run 'Truncate', I get a completely different B value at 27.3, which is obviously much better. However, why did I have to do this, and where would I find this value at the end of my refinement? i.e. did I miss a line in PROCHECK or my final REFMAC log file?
Thank you all,
Jim
--- On Wed, 8/20/08, Lijun Liu <[log in to unmask]> wrote:
> From: Lijun Liu <[log in to unmask]>
> Subject: Re: [ccp4bb] Lower completeness, decent R factors, but low B factor...
> To: [log in to unmask]
> Date: Wednesday, August 20, 2008, 1:32 PM
> 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
> <[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..
> >
> >
> >
>
> Lijun Liu, PhD
> Institute of Molecular Biology
> HHMI & Department of Physics
> University of Oregon
> Eugene, OR 97403
> 541-346-4080
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