Hi Sarathy, What does the density modified electron density map after phasing from either autoSHARP or Phenix? Can the auto building programs build protein chains into this map?
Cheers, Scott On Nov 30, 2012, at 5:27 PM, Sarathy Karunan Partha <sarathyus...@gmail.com<mailto:sarathyus...@gmail.com>> wrote: Dear all, Here is the XSCALE.LP output after scaling for the izit dye stained crystak. Sorry for attaching the .INP file. Sarathy On Fri, Nov 30, 2012 at 4:19 PM, Sarathy Karunan Partha <sarathyus...@gmail.com<mailto:sarathyus...@gmail.com>> wrote: Dear all, We did some Izit dye staining to test our crystal (salt or protein) and we observed that the crystal didn’t take up the dye well. But, showed nice protein diffraction (home source KCr 2.2909 A) and we collected a dataset (360 frames, 1o osc, 5 min exposure) on this dye stained crystal. The data collection statistics looks great and most interestingly we saw some anomalous signal for this data (see attached XSCALE.LP). This protein was crystallized in 0.2 M Ca acetate, 30 % PEG 400 pH 4.5. Izit dye is basically methylene blue which contains a sulfur atom (phenothiazine ring) and also has some basic dimethylamio groups. Our protein has many acidic residues that could enhance binding of this basic dye.We think the anomalous signal could be from this dye and the heavy atom search with autoSHARP and Phenix autosol is suggestive of 4 sulfur atoms. Did anyone come across similar situation with using this dye and also welcome any suggestions about using this data for S-SAD phasing. Thanks, Sarathy <XSCALE.LP> ******************************************** Scott T. R. Walsh, Ph.D. Assistant Professor University of Maryland College Park Dept of Cell Biology and Molecular Genetics Institute for Bioscience and Biotechnology Research Rm 3127E SG II 9600 Gudelsky Drive Rockville, MD 20850 email: swals...@umd.edu<mailto:swals...@umd.edu> phone: (240) 314-6478 fax: (240) 314-6255
