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, 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

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