Re: [ccp4bb] High overall b-factor

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: High overall b-factor
From: George Lountos gt2933a {- at -} HOTMAIL {- dot -} COM
Date: 2007-03-09

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Subject: Differences in R and Rfree
From: Nicholas Noinaj noinaj {- at -} UKY {- dot -} EDU
Date: 2007-03-09

Subject: Re: High overall b-factor
From: ezra peisach epeisach {- at -} MED-XTAL {- dot -} BU {- dot -} EDU
Date: 2007-03-09

I have never worked at 3.2A - but I suspect that the overal temperature
factor is being determined from the slope of a Wilson plot. However,
Wilson plots only really "work" at higher resolution (2.8 or better). Look
at the output from truncate and see what it is predicting - and look at
the plot - it should be pretty obvious why you have such a high B.

Ezra

On Fri, 9 Mar 2007, George Lountos wrote:

>
> Hello all:
>
> I just recently collected data on initial crystals I grew of an enzyme
> with inhibitor. The crystals diffract to only 3.2 A but I was able to get
> phases by molecular replacement to see if there is any inhibitor bound.
> Although the data processed well in HKL2000 with good statistics and the
> current structure refinement is at R-factor of 22% and R-free 30% at 3.2
> A, the overall B-factor of the protein is very, high (100 A^2). I can see
> difference density for the ligand in the active site and after refinement
> it fits well in the density but the B-factor for the ligand is 110. I
> have not come across a refinement with such high B-factors where the
> protein density and ligand density can be distinguished at such high
> B-factors. Does anyone have any suggestions if there is something going
> wrong here?
>
> Thanks,
>
> George
>
>
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: High overall b-factor
From: George Lountos gt2933a {- at -} HOTMAIL {- dot -} COM
Date: 2007-03-09

Next message:
Subject: Differences in R and Rfree
From: Nicholas Noinaj noinaj {- at -} UKY {- dot -} EDU
Date: 2007-03-09