Another question: since during data collection the chlorine disappears, can the residues surrounding the chlorine adjust their position to compensate for the vanishing of the atom? Can the ligand move? Do things move during data collection?
Meaning, can I describe what I see in my structure as a structure that have in its active site a ligand with a chlorine....even if it is really not there? ...but it was there during crystal growth...? Thanks again, Eli PS: I will read your answers tomorrow! GRAZIE GRAZIE!!!!!!! On Thu, November 29, 2007 5:04 pm, Sabini, Elisabetta wrote: > Thank you for all the answers I am starting to get! > In the meantime, could I please also ask you to suggest to me papers that > would be a good reference to put in my publication? > Thank you again! > Eli =) > > > On Thu, November 29, 2007 4:21 pm, Fischmann, Thierry wrote: >> Dear Eli, >> >> I work in a pharmaceutical company and go through many diverse >> compounds. >> My extensive experience with Br and Cl is that they easily get cleaved >> by >> X-ray. I've done a lot of experiments to address the problem: radical >> scavengers (fail: it does not look like the process is >> radical-mediated), >> energy dependence (fails: in fact cleavage occurs at the home Cu 1.54Å >> source), and fast data collection (success at the expense of data >> quality, >> but often mandatory). >> >> Cleavage happens much more readily if the halogen is exposed to solvent. >> In fact I have "the ultimate proof" that this is a determinant factor: a >> chiral compound which changes binding orientation when the chirality is >> inversed, and the halogen either exposed to solvent or buried depending >> on >> chirality. That atom is connected to a non-chiral, planar moiety, >> therefore its chemical environment is the same in each enantiomer. >> However >> cleavage is very fast in the solvent-exposed conformation, and very slow >> in the opposite orientation. >> >> Solutions: >> - Collect your data very quickly (example: after running a strategy, 1 >> second exposure for 1 degree sweep at the synchrotron, for a total sweep >> of 100 deg). The cleavage is clearly dose-dependent. >> - Re-scale your data after discarding data collected at the end. Often >> (but not always) these data add redundancy but do little to >> completeness. >> Try to discard as much data as possible while keeping the completeness >> reasonable. I wouldn't be surprised that the #1 structure would do much >> better in terms of Cl occupancy if you could get by with 50% of the >> data. >> #2 may be a more tricky case. >> >> As far as publication is concerned, I wouldn't show the Cl for #2, but I >> would show it for #1 if there is no indication that the binding pose has >> moved due to cleavage. That is the case for my compounds. >> >> Good luck! >> Thierry >> >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of >> Sabini, Elisabetta >> Sent: Thursday, November 29, 2007 04:41 PM >> To: [email protected] >> 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 message and any attachments are solely for the >> intended recipient. If you are not the intended recipient, >> disclosure, copying, use or distribution of the information >> included in this message is prohibited -- Please >> immediately and permanently delete. >> >> > > > -- > 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] > > > -- 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]
