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On 04/07/2014 03:16 PM, Eugene Valkov wrote:

Thanks for the input, Eugene. No, these do not impact phasing or refinement significantly. We've SAD phased data like these with 5-Br and 5-I dU with no problems. The refinement is a bit tricky for some of the structures because they are lower resolution and the space group is pretty small, but that isn't related to the streakiness.


--p

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Paul,

The fibre-like characteristics present in some diffraction patterns of nucleic acids, which I think you are referring to, is the contribution of the helical transform of the double-stranded helix. Essentially, the length of the regular spacings in the base pairs modulates the intensities of the Bragg reflections. These then do not decay smoothly as the function of resolution which results in intensities along the helical axes at 3.4A being quite strong whilst perpendicular ones are much weaker. I have observed this in the diffraction patterns of RNA crystals but I have not seen the diffuse streaking along lattice lines that you show.

One recent example of fibre-like diffraction of a nucleic acid is illustrated here:

https://drive.google.com/file/d/0B-wXJqcqFfUHUVpvZDhqREdqMzA/edit?usp=sharing

I do not think that what you are seeing in your crystals can be attributed solely to the above. The streaking between the spots is probably some sort of lattice anomaly. It would be interesting to hear if this had impacted in some way on phasing or refinement of the structure.

Eugene




On 7 April 2014 19:03, Paul Paukstelis <[log in to unmask]> wrote:
Seeing the diffuse streaking threads that have cropped up recently got me to thinking about many of the DNA data sets we have collected on. We always see diffuse streaking along lattice lines.

See images:

http://vespa.chem.umd.edu/~paul/hex_streak01.png
http://vespa.chem.umd.edu/~paul/hex_streak02.png
http://vespa.chem.umd.edu/~paul/hex_streak03.png

My original interpretation of this as fiber diffraction from alignment of DNA bases came after reading Doucet et al. Nature 337, 190-192 and seeing that the streaks start at around 3.4A and orientation of the helical portions of the structure are perpendicular to the six-fold. I didn't really give it much more thought till seeing the threads about diffuse streaking. These show up even in crystals that diffract to higher resolution than the one shown in the images. I wonder if this is actually something else given that they are along lattice lines? Opinions?

--paul



--
Dr Eugene Valkov

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