Sorry - hadnt finished.. The twinning tests are distorted by NC translation - usually the L test is safe, but the others are all suspect..
On 11 March 2014 14:09, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > What is the NC translation? If there is a factor of 0.5 that makes SG > determination complicated.. > Eleanor > > > On 11 March 2014 14:04, Stephen Cusack <cus...@embl.fr> wrote: > >> Dear All, >> I have 2.6 A data and unambiguous molecular replacement solution for >> two copies/asymmetric unit of a 80 K protein for a crystal integrated >> in P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9. >> Refinement allowed rebuilding/completion of the model in the noraml way >> but the R-free does not go below 30%. The map in the model regions looks >> generally fine but there is a lot >> of extra positive density in the solvent regions (some of it looking like >> weak density for helices and strands) and unexpected positive peaks within >> the model region. >> Careful inspection allowed manual positioning of a completely different, >> overlapping solution for the dimer which fits the extra density perfectly. >> The two incompatible solutions are related by a 2-fold axis parallel to a. >> This clearly suggests some kind of twinning. However twinning analysis >> programmes (e.g. Phenix-Xtriage), while suggesting the potentiality >> of pseudo-merohedral twinning (-h, l, k) do not reveal >> any significant twinning fraction and proclaim the data likely to be >> untwinned. (NB. The programmes do however highlight a >> non-crystallographic translation and there are systematic intensity >> differences in the data). Refinement, including this twinning law made no >> difference >> since the estimated twinning fraction was 0.02. Yet the extra density is >> clearly there and I know exactly the real-space transformation between the >> two packing solutions. >> How can I best take into account this alternative solution (occupancy >> seems to be around 20-30%) in the refinement ? >> thanks for your suggestions >> Stephen >> >> -- >> >> ********************************************************************** >> Dr. Stephen Cusack, >> Head of Grenoble Outstation of EMBL >> Group leader in structural biology of protein-RNA complexes and viral >> proteins >> Joint appointment in EMBL Genome Biology Programme >> Director of CNRS-UJF-EMBL International Unit (UMI 3265) for Virus Host >> Cell Interactions (UVHCI) >> ********************************************************************** >> >> Email: cus...@embl.fr >> Website: http://www.embl.fr >> Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 >> >> Fax: (33) 4 76 20 7199 >> Postal address: EMBL Grenoble Outstation, 6 Rue Jules Horowitz, BP181, >> 38042 Grenoble Cedex 9, France >> Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, >> 6 Rue Jules Horowitz, 38042 Grenoble, France >> ********************************************************************** >> > >
