Dear Pavel, Is this density located on a symmetry axis? There is quite often a lot of "noise" around these regions - and it may not, in fact, be possible to model this satisfactorily.
Tony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Feb 25, 2013, at 10:03 AM, Natashin Pavel wrote: > Hello everyone, > > > I’m working on a structure with a 1.72Å resolution data and almost finished > it. But there is a piece of unknown density between two protein molecules. > The following pictures show this density from two sides: > > http://www.4sync.com/photo/WHewU7Ek/Density_1.html > > > http://www.4sync.com/photo/RM3IEesw/Density_-_2.html > > This density is located between two protein molecules and is not connected to > either of them. > > I have tried to fit several small organic molecules from crystallization > conditions and protein sample buffer, also tried ligand database search using > “Phenix ligand identification” software, but no satisfactory results. > Crystallization condition: DL-Malic acid > > Sample Buffer: Bis-Tris, EDTA > > Reagents from protein purification step (also checked): Tris, Urea, > Triton-X100, DTT. > > > > I will very much appreciate to hear any suggestions and ideas on what to do. > > Best regerds, > > Pavel V. Natashin > > > PhD student > Photobiology Laboratory > Institute of Biophysics > Russian Academy of Sciences Siberian Branch > Krasnoyarsk 660036, Russia > > National Laboratory of Biomacromolecules > Institute of Biophysics Chinese Academy of Sciences > Beijing 100101, China
