On 20 Aug 2008, at 18:24, 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.
The first thing that I do with my data after coming back from the
synchrotron is process them nice and quite.
I know the selling point of synchrotrons that you go away with your
data processed all too well,
but the current reality of sample changers and ultra fast detectors
does not allow time to do the job on site
in an optimal fashion, in many cases. I would not be exaggerating to
say that every single dataset at NKI over the last 8 years,
we have processed again back at home to be sure we did things the
best possible way.
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?
Most likely the following is clear to you and most readers, but just
to be sure we are talking about the same things:
1. I was talking about Wilson B in my first answer, which would be
affected directly from missing weak reflections.
2. I see now you are talking about the mean B of all atoms, which I
am not sure how it would be affected by missing reflections
3. In your last email you go back (?) talking about Wilson B
(TRUNCATE) which is a whole different think than the mean B value of
all atoms you mentioned first.
Wilson B: property of your data, gradient of the fall-off of
Intensity as a function of resolution
Mean B of all atoms: property of your model, average B of all atoms
"For good data and a good model the two should not be too far apart"
Best, Tassos
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..
