 |
 |
I wish I could give a sensible explanation, but this feature is very common with heavy atoms. Possible problems. The default wavelength for all atomic scattering functions is Cu Ka - you can see the formula used and details in the file $CLIBD/atomsf.lib. The atomic scattering values are much the same for C N O at a range of wavelengths, but metals can have significant f' differences. You can correct this in REFMAC input - see documentation. The Zn is not fully occupied - this depends on how it is incorporated. Eleanor On 28 Aug 2012, at 18:44, Deepthi 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