Hi Rafal I think this is very important -
> - I back to images. I tried to index it again under iMOSFLM. Of course, the > most probably solutions are identical with those from XDS, but predictions > don't cover all spots on images. In addition I observed two or three spots in > the line on some images, with short distances between them, so for me it can > suggests much longer cell dimension in one direction. Maybe there is an > explanation. But when I tried add some spots manually, usually iMOSFLM > couldn't estimate cell parameters… If XDS and iMosflm are giving you the same cell (within a small error), but you can see regularly spaced spots between the predictions, then the cell found by indexing is probably smaller than the real cell. Even if that isn’t true, it would be useful for an expert to have a look at the raw data so they can give you a diagnosis. If I were you, at this point I would ask someone with more experience in processing data (perhaps the author of your favourite program (mine’s Mosflm….)) if they could have a look at a sample of your images to see if they can process the data in a way that predicts the vast majority of the diffraction spots. > > Best regards, > > Rafal > > --- > |----------------------------------------------| > |Rafal Dolot, Ph.D. | > | | > |Polish Academy of Sciences | > |Centre of Molecular and Macromolecular Studies| > |Department of Bioorganic Chemistry | > |Macromolecular Crystallography Team | > |Sienkiewicza 112 | > |90-363 Lodz, Poland | > |Phone: +48(42)6803215 | > |Cell: +48 502897781 | > |----------------------------------------------| > > W dniu 2018-04-21 23:02, Phoebe A. Rice napisał(a): >> Sadly Rafal is right the unit cell dimensions don't make sense - >> either the space group is wrong or the contents have been digested >> before crystallization. >> The size of the overall unit cell is ~21 x 23 x 43. Given a >> (DNA-centric but close enough) view that a duplex is ~25A wide and >> there are 3.4A per bp (and 43A/3.4 gives 12bp) , if this 11mer was a >> simple symmetric duplex, there could only be 2 chains, max, but I222 >> has 8 asymmetric units. >> This handy tool gives the same answer in a more accurate manner: >> http://csb.wfu.edu/tools/vmcalc/vm.html >> It says that if the RNA is intact and the space group is P2, there is >> about 56% solvent. If the space group is really I222, the solvent >> content would be a rather fascinating negative 75%. >> -Phoebe >> On 4/20/18, 2:37 PM, "CCP4 bulletin board on behalf of Randy Read" >> <CCP4BB@JISCMAIL.AC.UK on behalf of rj...@cam.ac.uk> wrote: >> I think that starting with a direct methods program like shelxt >> would be fun. If that doesn’t work, it could be interesting to try to >> solve it by molecular replacement with fragments varying from a >> tetraplex, a base pair or even just single bases. (Assuming that >> Phoebe’s concern about twinning does not turn out to be correct…) >> Best wishes, >> Randy Read >> ----- >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> Wellcome Trust/MRC Building Fax: +44 1223 336827 >> Hills Road >> E-mail: rj...@cam.ac.uk >> Cambridge CB2 0XY, U.K. >> www-structmed.cimr.cam.ac.uk >> > On 20 Apr 2018, at 20:09, Tim Gruene <tim.gru...@psi.ch> wrote: >> > >> > Dear Rafal, >> > >> > shelxt does not require the space group, it only needs the Laue >> group. If it >> > finds a decent solution, it'll find also the space group for you. >> > >> > Best, >> > Tim >> > >> > On Friday, April 20, 2018 3:30:36 PM CEST Rafal Dolot wrote: >> >> Dear CCP4BB, >> >> >> >> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, >> and >> >> DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell >> >> dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this >> >> size of the molecule. 11mer is rich in G, so we expect the G-tetraplex >> >> formation. Data were collected to almost 1 A, so it should be enough >> for >> >> trials with direct methods/ab initio solution. What I should do first >> to >> >> find correct SG and/or cell parameters? >> >> >> >> Best regards, >> >> >> >> Rafal >> > >> > -- >> > -- >> > Paul Scherrer Institut >> > Tim Gruene >> > - persoenlich - >> > OSUA/204 >> > CH-5232 Villigen PSI >> > phone: +41 (0)56 310 5297 >> > >> > GPG Key ID = A46BEE1A
