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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 > > > 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] > <mailto:[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/%7Epaul/hex_streak01.png> > http://vespa.chem.umd.edu/~paul/hex_streak02.png > <http://vespa.chem.umd.edu/%7Epaul/hex_streak02.png> > http://vespa.chem.umd.edu/~paul/hex_streak03.png > <http://vespa.chem.umd.edu/%7Epaul/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 > > Room 3N049 > Division of Structural Studies > > MRC Laboratory of Molecular Biology > Francis Crick Avenue > Cambridge Biomedical Campus > Cambridge CB2 0QH, U.K. > > Email: [log in to unmask] <mailto:[log in to unmask]> > Tel: +44 (0) 1223 267358