Rajesh, Ca2+ usually is coordinated by five atoms, whereas Mg2+ usually is coordinated by six. I've seen that a lot in structures that I've determined.
-Daniel On Wed, Mar 7, 2018 at 2:14 PM, Eleanor Dodson < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > You just calculate a anom map - it doesnt need you to dselect Ca or Mg or > anything else.. > Judge the peak heights by the signal you get over any S sites in the > model. The relative signal you expect depends on your wavelength of course. > Eleanor > > > On 7 March 2018 at 19:09, Rajesh Kumar <rajesh.p...@gmail.com> wrote: > >> Hi Ivan, >> >> https://csgid.org/csgid/metal_sites/ >> >> suggest that Mg++ is the correct metal. Ca++ is not acceptable. >> >> I am going to validate it by calculating anomalous peak for Ca++ too. >> >> Thank you >> Rajesh >> >> >> On Wed, Mar 7, 2018 at 1:06 PM, Ivan Shabalin < >> iva...@iwonka.med.virginia.edu> wrote: >> >>> Hi, Rajesh, >>> >>> It does look like Ca to me. It has around 2.4 A distances to waters and >>> quite many electrons (18), which correspond to rather wide and high density >>> peak in the middle. >>> >>> Mg has distances at 2.07, and 10 electrons (should be a smaller peak). >>> >>> Na has 2.41 distances to waters, 10 electrons (should be a smaller peak). >>> >>> After you place a metal and refine it, try using CheckMyMetal to >>> validate it: >>> >>> https://csgid.org/csgid/metal_sites/ >>> >>> >>> It takes into account preferable coordination geometries, coordination >>> bond distances, and compares ADPs to average ADP for the surrounding atoms. >>> >>> If the dataset is very good, and the wavelength of X-ray is rather long, >>> you might even get anomalous signal for Ca: >>> >>> http://skuld.bmsc.washington.edu/scatter/AS_periodic.html >>> >>> Ivan >>> >>> >>> >>> With best regards, >>> Ivan Shabalin, Ph.D. >>> Research Scientist, >>> Department of Molecular Physiology and Biological Physics, >>> University of Virginia, >>> 1340 Jefferson Park Avenue >>> <https://maps.google.com/?q=1340+Jefferson+Park+Avenue&entry=gmail&source=g>, >>> Pinn Hall,Room 4223, >>> Charlottesville, VA 22908 >>> >>> On 03/06/2018 05:19 PM, Rajesh Kumar wrote: >>> >>>> Dear All, >>>> >>>> Have you had experience with this kind of density? I am wandering what >>>> this could be? >>>> >>>> Thank you very much for the help. >>>> >>>> -Rajesh >>>> >>>> >>>> >>>> >>>> >>> ---- >>> >> >> >
