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
