Well - I have found lots of molecules but usually not in a single run. The first thing to think about is: is this likely to be a dimer? trimer? tetramer? Things to consider - a) any non-cryst translation? b) tthe self rotation might give a clue - c) is the model a multimer, c)what do the biochemists suggest? etc etc - If you are looking for a dimer say - the try searching with it.. Eleanor
On 30 April 2012 17:33, David Schuller <dj...@cornell.edu> wrote: > On 04/30/12 11:41, Ke, Jiyuan wrote: > > Dear All,**** > > ** ** > > I have a question regarding solving a crystal structure by molecular > replacement. It is a single protein with a molecular weight of 25.5 kDa. > The cell dimension is rather big from the diffraction data ( 90.9 Å, 143.9 > Å, 216.3Å, 90°, 90°, 90°). The possible space group is P212121. With such > a big unit cell, we predicted that there are 8-10 molecules per asymmetric > unit. We have a decent model with sequence similarity of 49%. I tried > several times with Phaser search with the current model and had difficulty > to find any clear solution. Has anyone seen such cases and any suggestions > to solve the structure? Thanks!**** > > ** ** > > I solved 8 copies with 32% identity to the search model (1ZL9). I used > BEAST for the MR, in the days before Phaser. > > You say you have a single protein, which I interpret to mean that the > active unit is a monomer. Bummer, searching with a multimer would certainly > simplify things. > > See that your search model is compact. Is the search model a single > domain? Does the sequence similarity extend throughout the entire thing? > Are there loops which should be clipped? > > With such a large number of monomers, translation-only NCS seems likely, > so be on the lookout for that. > > -- > ======================================================================= > All Things Serve the Beam > ======================================================================= > David J. Schuller > modern man in a post-modern world > MacCHESS, Cornell University > schul...@cornell.edu > >
