Re: [ccp4bb] modelling with sad/mad data

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

Previous message:
Subject: Re: Differences in R and Rfree
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-19

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Subject: Re: RMSD
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-19

Subject: Re: modelling with sad/mad data
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-19

First it is always best to refine your model against the highest
resolution good quality data that you have available. There was
correspondence about the geometric weighting - could you have weighted
the Xray data too high and have bad geometry - see previous Emails!

And the Free R seems rather low for the Se data.
Did you transfer the same Free R set from the native to the Se data?
Eleanor

Peng Zhang wrote:
> Dear friends,
>
> Recently, I have solved a structure using mad method. When using the peak
> data(2.3A) as the native for structure refinement, the gap between R
> factor and R free is big, about 0.1(0.22 and 0.32). I modelled the
> selenomethionine but the gap still exists. When I changed the data for a
> real native one(2.7A),it seems OK with R=0.24 and Rf=0.28.
>
> Does anyone have the similar experience?
> what should I pay attention to when using the sad/mad data as the native
> one for modelling and refinement?
>
> Thanks in advance.
>
>
>

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

Previous message:
Subject: Re: Differences in R and Rfree
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-19

Next message:
Subject: Re: RMSD
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-03-19