[phenixbb] Defining planarity for Phenix.refine

Francis E Reyes Francis.Reyes at Colorado.EDU
Mon Apr 19 11:56:01 PDT 2010

On Apr 19, 2010, at 11:50 AM, Nathaniel Echols wrote:

> On Mon, Apr 19, 2010 at 8:50 AM, Engin Özkan <eozkan at stanford.edu>  
> wrote:
> I should say that I have never worked with DNA in crystal  
> structures, and due to its structure, it might be better suited to  
> parameterization that allows accurate rigid bodies. I just don't know.
> I'm not a nucleic acid crystallographer either, but aren't the  
> helices (especially A-form) significantly more flexible than, say, a  
> protein alpha-helix (or entire globular domain)?

Let's be clear on what is meant by 'flexible'. In solution,  A-form  
RNA helicies are generally not flexible. They're fairly rigid in  
solution and that can be observed by many of inline probing experiments.

Now let's talk about flexibility during refinement. Without  
restraining the bases with some kind of strict geometry weight, or in  
the case of the OP, specifically restraining coplanar base pairing for  
canonical watson crick pairing, depending on the quality of the  
phases, I've seen phenix.refine and refmac pull bases that we know to  
be base paired in an A-form helix out of the 'coplanar base pair'  
orientation. If I were solving an RNA from scratch, I'd know apriori  
that this is a true base pair, and it's almost offensive that a  
refinement program would say otherwise. It's not drastic, but any RNA/ 
DNA structural biologist will look at your structure and clearly see  
that there's something wrong with the geometry.   While it maybe a  
minor nuisance to correct this manually, I can only wonder how it  
affects the refinement.


Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

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