Oops. I meant to say that Ca2+ usually has seven coordinating atoms. Mg2+ usually has six. Sorry for the error.
-Daniel On Wed, Mar 7, 2018 at 2:27 PM, Daniel M. Himmel, Ph. D. < danielmhim...@gmail.com> wrote: > 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>> ---- >>>> >>> >>> >> >
