Re: [ccp4bb]: How to evaluate local coordinate error (?)

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

James Stroud wrote:
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> This is not a question directly related to ccp4 as far as I can tell, but I'm hoping someone on this list may have some insight.
> 
> We are presently working on the structure of a mutant wherein this mutant appears to have the rigid body movement of a 15 residue alpha-helix by about 1 Angstrom relative to the position of the helix in the wild-type. This movement is "detected" by the 2.5 sigma density of a simulated annealing fofc omit map. The problem is that our reflection data is 2 sigma only to about 3.2 Angstroms. So my questions are: How valid are any conclusions derived from this perceived movement? Is there a mathematical/statistical basis for such conclusions. If any person has a reference, I would be grateful. Or, almost as helpful would be for someone to restate my problem in the proper terminology so that I may do my own research. Of course a flat-out answer would be wonderful.
> 
> Thank you in advance for your help,
> 
> James
> --


 Seems pretty crystallographic to me!

 I think you could reasonably do rigid body refinement at 3.2A where the
helix was one of the bodies. You may want to break up the protein into
other suitable domains if that is appropriate. This would give you a
figure to quote - the helix should move and the R factor improve... You
can hardly quote coordinate errors for individual atoms at 3.2A but the
above  is a valid procedure I think.


Eleanor

> --------------------------------------------------------
>  James C. Stroud
>  Department of Chemistry and Biochemistry
>  University of Colorado at Boulder
>  Boulder, CO 80309
> 
>  Tel: 303-492-4503      Fax: 303-735-1347
> --------------------------------------------------------