Dear Pavel, you should also always consider your cryoprotectant molecules, so let's say if you used PEG for cryoprotection, there's a very high probability you may see it in your structure. It's very hard to say from the snapshots, but for the patch of density depicted in fig.2 I would try PEG (of course only if you had it). All the best, Albert
2013/2/25 Antony Oliver <antony.oli...@sussex.ac.uk> > 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 > >
