On Mon, Apr 19, 2010 at 8:50 AM, Engin Özkan <[email protected]> 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. 

F

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

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