What a beautiful and interesting diffraction pattern! To me, it seems that there is a blurred set of spots with different cell dimensions, although nearly the same, underlying the ordered diffraction pattern. A possible interpretation occurred to me, that the ordered part of the crystal is supported by a less-ordered lattice of slightly different dimensions, which, because the crystal is a like a layer-cake of 2-d crystals, need not be commensurable in the short range with the ordered lattice. The nicely-ordered "cake" part of the crystal you solved, but the "frosting" between is of a different, less ordered nature, giving rise to the diffuse pattern which has slightly different lattice spacing. I would have to see more images to know whether this apparent lattice-spacing phenomenon is consistent, but it at least seems that way to me from the images you put on the web. I would shudder to think of indexing it, however.
All the best, Jacob Keller ps I wonder whether a crystal was ever solved which had two interpenetrating, non-commensurable lattices in it. That would be pretty fantastic. ==============Original message text=============== On Mon, 27 Aug 2007 5:57:45 am CDT "Mark J. van Raaij" wrote: In general, I think we should be careful about too strong statements, while in general structures with high solvent diffract to low-res, there are a few examples where they diffract to high res. Obviously, high solvent content means fewer crystal contacts, but if these few are very stable? Similarly, there are probably a few structures with a high percentage of Ramachandran outliers which are real and similarly for all other structural quality indicators. However, combinations of various of these probably do not exist and in any case, every unusual feature like this should be described and an attempt made to explain/analyse it, which in the case of the Nature paper that started this thread was apparently not done, apart from the rebuttal later (and perhaps in unpublished replies to the referees?). With regards to our structures 1H6W (1.9A) and 1OCY (1.5A), rather than faith, I think the structure is held together by a real mechanism, which however I can't explain. Like in the structure Axel Brunger mentioned, there is appreciable diffuse scatter, which imo deserves to be analysed by someone expert in the matter (to whom, or anyone else, I would gladly supply the images which I should still have on a tape or CD in the cupboard...). For low-res version of one image see http://web.usc.es/~vanraaij/diff45kd.pngand http://web.usc.es/~vanraaij/diff45kdzoom.pngtwo possibilities I have been thinking about: 1. only a few of the "tails" are ordered, rather like a stack of identical tables in which four legs hold the table surfaces stably together, but the few ordered tails/legs do not contribute much to the diffraction. This raises the question why some tails should be "stiff" and others not; perhaps traces of a metal or other small molecule stabilise some tails (although crystal optimisation trials did not show up such a molecule)? 2. three-fold disorder, either individually or in microdomains too small to have been resolved by the beam used. For this I have been told to expect better density than observed, but maybe this is not true. we did try integrating in lower space groups P3, P2 instead of P321 with no improvement of the density, we tried a RT dataset to see if freezing caused the disorder and we tried improving the phases by MAD on the mercury derivative, but with no improvement in the density for the tail. Mark J. van Raaij Unidad de Bioquímica Estructural Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ On 24 Aug 2007, at 03:01, Petr Leiman wrote: > ----- Original Message ----- From: "Jenny Martin" > <[EMAIL PROTECTED]> > To: <[email protected]> > Sent: Thursday, August 23, 2007 5:46 PM > Subject: Re: [ccp4bb] The importance of USING our validation tools > >> My question is, how could crystals with 80% or more solvent >> diffract so well? The best of the three is 1.9A resolution with I/ >> sigI 48 (top shell 2.5). My experience is that such crystals >> diffract very weakly. > > You must be thinking about Mark van Raaij's T4 short tail fibre > structures. Yes, the disorder in those crystals is extreme. There > are ~100-150 A thick disordered layers between the ~200 A thick > layers of ordered structure. The diffraction pattern does not show > any anomalies (as far as I can remember from 6 years ago). The > spots are round, there are virtually no spots not covered by > predictions, and the crystals diffract to 1.5A resolution. The > disordered layers are perpendicular to the threefold axis of the > crystal. The molecule is a trimer and sits on the threefold axis. > It appears that the ordered layers somehow know how to position > themselves across the disordered layers. I agree here with Michael > Rossmann that in these crystals the ordered layers are held > together by faith. > Mark integrated the dataset in lower space groups, but the > disordered stuff was not visible anyway. He will probably add more > to the discussion. > > Petr > > >> >> Any thoughts? >> >> Cheers, >> Jenny ===========End of original message text=========== *********************************** Jacob Keller Northwestern University 6541 N. Francisco #3 Chicago IL 60645 (847)467-4049 [EMAIL PROTECTED] ***********************************
