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
