I'm not sure that a library of ligand electron density would be an entirely good thing. I guess something small like an acetate or DMSO would be relatively consistent but larger things like PEGS or even glycerols are going to be dependent on the nature of the binding site. A good example would be to look at something that binds ATP as an enzymatic co-factor versus a binding protein. Completely different geometry.
For a beginner I'd suggest to always check your difference peaks and all your waters between rounds of refinement. If the positive density peaks are covalent bond distance apart, it's not a water. If you've got giant green smears between or around your "waters" it might not be a water. If you've got good enough density and can guess at a basic framework you can plug a rough sketch into the chemical structure search function in PubChem that can give you some possible options. You can cross-reference the hits to the HIC-Up server or the PDB for restraints or density examples keeping in mind that your ligand-protein interactions may be different. Also do a sanity check and ask yourself "does this make chemical sense?" If you've modeled something in there is TWILIGHT to see if your density supports your model. Of course there is also experimental evidence but that's a different can of worms. Basically really look at your data and if something seems hinky then look for alternatives. My $0.02, Katherine On Tue, May 21, 2013 at 3:05 PM, Jeffrey, Philip D. <pjeff...@princeton.edu>wrote: > Top 20 HETNAM entries based on 58,469 PDB entries at better than 2.5 > Angstrom resolution (arbitrary cut): > > Number of entries in histogram: 14864 > Total number of instances : 195481 > > 0 14502 0.0742 GOL (glycerol) > 1 10952 0.0560 SO4 > 2 8064 0.0413 ZN > 3 7628 0.0390 MG > 4 6930 0.0355 MSE (SeMet) > 5 6685 0.0342 CA > 6 6555 0.0335 EDO (Ethylene glycol) > 7 6315 0.0323 CL > 8 5856 0.0300 HEM > 9 3922 0.0201 NA > 10 3647 0.0187 NAG > 11 3148 0.0161 PO4 > 12 2360 0.0121 ACT (Acetate) > 13 1874 0.0096 MN > 14 1561 0.0080 NAP > 15 1387 0.0071 K > 16 1338 0.0068 FAD > 17 1277 0.0065 PLP (PYRIDOXAL-5'-PHOSPHATE) > 18 1228 0.0063 TRS (Tris buffer) > 19 1205 0.0062 FMN > > (numeric columns are ranking; count; frequency) > No electron density, sorry. > Clearly I should be adding more glycerols. > > Phil Jeffrey > Princeton > > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 孙庆祥 [ > baby_ten...@163.com] > *Sent:* Tuesday, May 21, 2013 3:29 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] list/library of most commonly co-crystallized > ligands/solvents and/or their electron density shapes > > hi all, > > Sorry if this has been asked before. I wonder if there is an list or > library of most commonly co-crystallized ligands(or solvent molecules) > available? Better if the electron density maps of the ligands are also > shown with different resolutions. That could help a lot for an > inexperienced crystallographer (like me) to quickly identify extra electron > densities in a new structure, by simply comparing the electron density > shapes. > > I remember a few days ago somebody asked about a PEG electron density, > which looks like a string of beads. If I knew that earlier, I could have > modeled it in, instead of waters... > > Thanks, > Jeremy > > >
