Re: [ccp4bb] unknown density

[Roger Rowlett]

I agree with many others: this is quite possibly sulfate or phosphate. If collected at 1.54A the anomalous map should help identify the presence of sulfur. Sulfate or phosphate may be present at lower than full occupancy. I would refine everything else you reasonably know in the model (including water and any other anions, ligands, etc.) and see if the blob of density sharpens up. Usually a sulfate looks like a sphere of density, and a sulfate + water may be somewhat elongated. If the difference map without modeled anion looks reasonable, try a sulfate of phosphate at 1.0 or 0.5 occupancy to see if the 2Fo-Fc and Fo-Fc maps still look reasonable. There is plenty of precedent for sulfate/phosphate binding near Glu and Arg residues. If you have negative Fo-Fc density when using sulfate at 0.5 occupancy, you may have no other reasonable choice than to model with water (or nothing at all), with the acknowledgment that this may not be completely correct, either. Cheers. On 2/3/2010 12:17 PM, Katja Schleider wrote: Dear all, I found some fairly substantial density in the active site of my protein structure. But I don´t know what it should be. My crystallisation condition consists of lithium sulfate, citrate-phosphate and peg1000. The whole lot doesn't make a dashed bit of sense!  Any suggestions to fill this density with something? Picture is attached. Thanks a lot, Katja __________________________________________________ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu