Dear Kumar, If you build the sites as Ca2+, you can use a few things for validation: - Ca2+ ions are exclusively coordinated by oxygens - The bond valance method (implemented in e.g. WASP and WHAT_CHECK) can be used to check whether a calcium ion makes sense. Do this before (reciprocal space) refinement because the VDW restraints may bias the atomic distances - Zn refined as calcium will have a suspiciously low B-factor.
Note that if the site is not fully occupied or contains a mixture, it will become complicated. Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Kumar, Veerendra > Sent: Tuesday, October 30, 2012 19:56 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Ca or Zn > > 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
