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 > ********************************************************************** >
