Sent using BlackBerry® from Orange -----Original Message----- From: Jacob Keller <j-kell...@fsm.northwestern.edu> Sender: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Date: Tue, 24 Jul 2012 12:55:31 To: <CCP4BB@JISCMAIL.AC.UK> Reply-To: Jacob Keller <j-kell...@fsm.northwestern.edu> Subject: Re: [ccp4bb] How to identify unknow heavy atom??
Perhaps also exafs should be mentioned--I believe the various ion species, redox states, and even binding geometry can be determined. JPK On Tue, Jul 24, 2012 at 12:37 PM, Roberts, Sue A - (suer) < s...@email.arizona.edu> wrote: > Hello > > Actually, if the home source uses a copper tube, neither copper nor zinc > have much of an anomalous signal at that wavelength (the energy is below > the absorption edge for both). > The best way is to check the location of the absorption edge at the > synchrotron. Cu+ and Cu++ can be distinguished this way, but make sure the > absorption scan is done before you collect data since copper(II) can be > photoreduced to copper(I) in the synchrotron x-ray beam. Whether or not > you can get a clue from geometry depends upon the resolution of the > structure. > > Sue > > On Jul 24, 2012, at 10:22 AM, Nat Echols wrote: > > > On Tue, Jul 24, 2012 at 10:14 AM, Haytham Wahba <haytham_wa...@yahoo.com> > wrote: > >> 1- if i have anomalous peak of unknown heavy atom, How can i identify > this > >> heavy atom in general. (different methods) > >> > >> 2- in my case, i see anomalous peak in heavy atom binding site (without > any > >> soaking). preliminary i did mass spec. i got Zn++ and Cu, How can i know > >> which one give the anomalous peak in my protein. > >> > >> 3- there is way to know if i have Cu+ or Cu++. > > > > You may be able to identify the element based on the coordination > > geometry - I'm assuming (perhaps incorrectly) that it is actually > > different for Cu and Zn. Marjorie Harding has written extensively on > > the geometry of ion binding: > > > > http://tanna.bch.ed.ac.uk/ > > > > The only way to be certain crystallographically, if you have easy > > access to a synchrotron, is to collect data above and below the K edge > > of any candidate element, and compare the difference maps. (For > > monovalent ions it is more complicated, since they don't have > > accessible K edges.) On a home source, Cu should have a larger > > anomalous map peak, but I'm not sure if this will be enough to > > identify it conclusively. > > > > -Nat > > Dr. Sue A. Roberts > Dept. of Chemistry and Biochemistry > University of Arizona > 1041 E. Lowell St., Tucson, AZ 85721 > Phone: 520 621 8171 or 520 621 4168 > s...@email.arizona.edu > http://www.cbc.arizona.edu/xray or > http://www.cbc.arizona.edu/facilities/x-ray_diffraction > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *******************************************
