Dear Elisabetta, Which program did you use for refinement? If you used REFMAC, the atomic scattering factors are internally coded for copper radiation, and the resulting electron density map after refinement may be much lower for halide atoms than it should be! It is a known REFMAC issue. Tadeusz
"Sabini, Elisabetta" <[EMAIL PROTECTED]> Sent by: "CCP4 bulletin board" <CCP4BB@JISCMAIL.AC.UK> 29-Nov-2007 21:40 Please respond to "Sabini, Elisabetta" <[EMAIL PROTECTED]> To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] "Finding Chlorine" =) Dear all, I am refining two structures which have in the active site a ligand containing a covalent bond between a carbon and a chlorine atom. I collected the data at APS, SERCAT ID-22. Because of radiation damage I tried different occupancy values for the chlorine atom and structure number #1 is best with occupancy 0.2 while structure #2 seems to be happy with occupancy 0 (occupancy for the rest of the ligand is 1). I checked by mass spec if my compound has the molecular weight expected with a chlorine atom and it does, so the original compound was correct. Can radiation damage make the chlorine completely disappear? Do the different occupancy values I get depend also on the resolution? In fact: Structure # 1 (OCC=0.2) refined to 1.8A (Rfact/Rfree=20/25%) Structure # 2 (OCC=0.0) refined to 2.5A (Rfact/Rfree=23/33%) When I make the figures for publication, do I draw the ligand with or without chlorine? Thanks, Eli =) -- Elisabetta Sabini, Ph.D. Research Assistant Professor University of Illinois at Chicago Department of Biochemistry and Molecular Genetics Molecular Biology Research Building, Rm. 1108 900 South Ashland Avenue Chicago, IL 60607 U.S.A. Tel: (312) 996-6299 Fax: (312) 355-4535 E-mail: [EMAIL PROTECTED] ----------------------------------------------------------- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. -----------------------------------------------------------
