On Fri, Jan 06, 2012 at 04:23:03PM +0800, ?????? wrote: > Also, there is one more information I forgot to mention---I also have the > NMR assignment(HNCACB spectrum) of the protein, is it possible to combine > the NMR data in my refinement?
Yes - we did something a few years back for the structure of the human voltage-dependent anion channel (slightly more reflections, but lower resolution) using a combination of Se-MET phases (SHARP), NMR and secondary-structure restraints in refinement (BUSTER). See Monika Bayrhuber, Thomas Meins, Michael Habeck, Stefan Becker, Karin Giller, Saskia Villinger, Clemens Vonrhein, Christian Griesinger, Markus Zweckstetter, Kornelius Zeth(2008): Structure of the human voltage dependent anion channel. Proc. Nat. Acad. Sci. USA 105: 15370-15375. or http://www.pnas.org/content/105/40/15370.full It contains a fair amount of background info about methods. Cheers Clemens > > Regards, > > On Fri, Jan 6, 2012 at 4:14 PM, ?????? <shangyuan5...@gmail.com> wrote: > > > Dear All, > > I have a set of 3.2A data containing only 3000 reflections. From the > > SAD phasing and iterative modeling and density modification, I get a > > preliminary structure with bad geometric conformations(~8/160 ramachandran > > outliers in Coot). After Phenix MLHL refinement, the geometry is still bad > > with (10% ramachandran outliers and 25% Rotamer outliers), and the > > B-factors are all too high(all between 80 to 170, average ~120), and > > R-factor/R-free have a value of 0.328/0.326. > > The poor geometry of my model and the unusual B-factors indicates there > > are still a lot improvement in my model. The question is, as I only have > > ~3000 reflections, and the atoms in the sequence is around 1000, and each > > atom there are 4 parameters to be refined(X,Y,Z,B-factor, > > assuming occupancy is 1), so how to refine my model to avoid > > over-refinement? Should I trust the electron-density map of the refined mtz > > data, or should I adjust the local geometries using Coot rotamers tools? > > How to set a reasonable B-factor values in the refinement? > > > > Best Regards, > > Yuan > > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
