Hi Deepthi, 1) refine anisotropic ADPs for Zn, 2) make sure charge is accounted for, 3) refine f' and f'' for Zn (that means you need to use anomalous data in refinement).
If 1-3 do not help, add 4) refine occupancy of Zn, 5) make sure you visualize your map using correct levels. This should solve the problem. Pavel On Tue, Aug 28, 2012 at 10:44 AM, Deepthi <deept...@gmail.com> wrote: > Hi everybody, > > I am working on a mutant protein structure which is 56 aminoacids long and > solved the structure using SAD( Single wavelength anomalous dispersion) > with zinc ions. We used SHELX software to locate the Zinc atoms and solved > phases. We got the structure as a monomer. The resolution of the structure > is 1.4 A0 . > > The problem with the structure is, when i calculate the structure factors > in COOT it always shows negative electron density around ZINC atoms which > have been located by SHELX. > > I initially thought it was because my COOT software was very old and it > doesn't recognize the Zinc atoms( I am new to crystallography) . I > calculated the structure factors using FFT from CCP4 and it shows the same. > I don't understand the problem. It refines well in Refmac and B-factors > also look very good. > > Anyone know what the problem is? > > Thank You in advance > Deepthi > > -- > Deepthi >
