probably that of course and unfortunatelly wilson plot will not work at that resolution, you need the linear bit. also one can always take a look at other less than 3 Å structures in the PDB... another question is how did you refine the b-factor, hopefully just an overall b-factor...?
this is probably best you can get at that resolution.. whether you can trust the ligand density depends on (size, shape and chemical properties of) the ligand. tommi Quoting ezra peisach <[EMAIL PROTECTED]>: > I have never worked at 3.2A - but I suspect that the overal temperature > factor is being determined from the slope of a Wilson plot. However, > Wilson plots only really "work" at higher resolution (2.8 or better). > Look > at the output from truncate and see what it is predicting - and look at > the plot - it should be pretty obvious why you have such a high B. > > Ezra > > > On Fri, 9 Mar 2007, George Lountos wrote: > > > > > Hello all: > > > > I just recently collected data on initial crystals I grew of an enzyme > > with inhibitor. The crystals diffract to only 3.2 A but I was able to > get > > phases by molecular replacement to see if there is any inhibitor > bound. > > Although the data processed well in HKL2000 with good statistics and > the > > current structure refinement is at R-factor of 22% and R-free 30% at > 3.2 > > A, the overall B-factor of the protein is very, high (100 A^2). I can > see > > difference density for the ligand in the active site and after > refinement > > it fits well in the density but the B-factor for the ligand is 110. I > > have not come across a refinement with such high B-factors where the > > protein density and ligand density can be distinguished at such high > > B-factors. Does anyone have any suggestions if there is something > going > > wrong here? > > > > Thanks, > > > > George > > > > > > > ________________________________________________________________________________ > > Get a FREE Web site, company branded e-mail and more from Microsoft > > Office Live! > > > -- Tommi Kajander, Ph.D. Macromolecular X-ray Crystallography Research Program in Structural Biology and Biophysics Institute of Biotechnology PO box 65 (Street address: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940
