Do occupancy refinement. Especially if you use the new "anomalous
refinement" option available in refmac, phenix.refine and other packages
as well, you should be able to get a pretty reliable number for how many
"real electrons" as well as "anomalous electrons" are at each site. At
almost any reasonable B-factor a Ca+2 looks a LOT like a Zn+2 at 64%
occupancy, and the f" will also be very different (depends on your
wavelength).
If the results are not abundantly clear, then you can get a kinda-sorta
"error bar" by starting refinement with different occupancies, and
perhaps "kicking" the starting model coordinates around (to "remove
bias"). If the occupancy keeps refining back to the same value, then
you can be reasonably confident that it is well-determined by your data.
If the occupancy doesn't appear to stably return to the "same" value, or
at least values different enough to say it is Zn vs Ca, then the
identity of your metal sites is NOT well-determined by your data.
-James Holton
MAD Scientist
On 10/30/2012 7:55 PM, Kumar, Veerendra wrote:
Dear CCP4bb users,
I am working on a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I
purified the protein in presence of Ca2+ and crystallized the Ca2+ bound
protein. I got crystal and solved the structure by SAD phasing at 2.1A
resolution. I can see the clear density in the difference map for metals at the
expected binding sites. However I had ZnCl2 in the crystallization conditions.
Now i am not sure whether the observed density is for Ca or Zn or how many of
them are ca or zn? Since Ca (20 elctron) and Zn (30 electron), is this value
difference can be used to make a guess about different ions?
is there any way we can find the electron density value at different peaks?
Thank you
Veerendra
