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Re: [ccp4bb] Strange behavior in R32 |
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CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 04 April 2007Subject: Re: Strange behavior in R32 From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA Date: 2007-04-04 In hexagonal R32 setting there is translational crystallographic symmetry leading to systematic absences. If you think Xtal 5 is basically the same but with slightly different packing that break the symmetry then you will have pseudo-translational symmetry leading to one set of very strong intensities (those that obey the hexagonal R32 lattice rules) and a set with very weak intensities (the once that are systematically absent in R32). That abundance of very strong and very weak intensities would give you a bimodal intensity distribution that would lead to the observed very large second moment in truncate. It is not immediately clear though what is going on with the other xtals. It may be of interest to look at the actual intensity distributions for different resolution slices to see if it is bimodal or not. Bart dklein@FHCRC.ORG wrote: > Dear Friends, > > I have some crystals of a small RNA in sg R32 that exhibit some bizzare > behaviors and fail to give phasing solutions. I am hoping someone out there > might be able to lend some insight. All crystals come out of the same condition > and look the same morphologically but, for reasons unknown and at this point > uncontrollable, have very different cell dimensions: > > Xtal 1: R32 77 x 77 x 80 Ang > Xtal 2: R32 77 x 77 x 86 Ang > Xtal 3: R32 78 x 78 x 366 Ang > Xtal 4: R32 78 x 78 x 460 Ang > Xtal 5: P3(1)21 77 x 77 x 85 Ang > > I've collect >95% complete datasets for each crystal form to resolutions between > 2.2-3.0 Ang. Denzo/scalepack outputs look fine in each case. Overall R-sym's > are okay (range is 8-13%). The only apparent red flag is the 2nd moment of I > calculated in truncate. These values are much larger than those expected for > either twinned (1.5) or untwinned (2.0) data: > > Xtal 1: 3.2 > Xtal 2: 2.5 > Xtal 3: 4.9 > Xtal 4: 3.7 > Xtal 5: 4.2 > > Also, use of the Yeates server to look for partial twinning tells me there are > no twin laws for R32, while the P3(1)21 data does not seem to be twinned. > > I'm guessing crystals 1 & 2 are very similar but still somewhat non-isomorphous, > and crystal 5 is also very similar with a breakdown in space group symmetry > that would put 3 mols/ASU instead of 1 mol/ASU as in R32. But I do not > understand what is going on with crystals 3 & 4. Has anyone out there > experienced similar non-integer multiples of a cell dimension for a given > crystal? I have covalently attached iodine in some of these crystal forms. But > no luck finding any sites by SAD, and I can't help but wonder if this funny > c-dimension behavior and/or the high > greater crystal pathology. > > Thanks in advance, > Dan > > -- ============================================================================== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================== CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 04 April 2007 |
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