Re: [ccp4bb]: maps have negative peaks around "heavy" atoms (Cu, Cl, S)

["Edward A. Berry" <EABerry@lbl.gov>]

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Sue,
Are there discrete negative peaks near the atom position 
in the difference map, or shells of negative density 
surrounding a positive peak at the atom position? 
I have the latter (or vice versa) at iron positions 
in a cytochrome, which I attribute to scalling problems.
Manually adjusting the B-factor for Fcalc in FFT can
smooth it out. 

Ed

Sue Roberts wrote:
> 
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> 
> Hello,
> 
> I've been refining a structure that contains Cu atoms. When I refine with refmac
> (using the ccp4 interface), R, Rfree are quite low (0.16, 0.19), and the "heavy"
> atoms (Cu, Cl, many S) have large (> 5 sigma) negative peaks around them. These
> are the largest 12 peaks in the difference map. They are located essentially at
> the atomic positions.
> 
> Data is complete to 1.7 A and was measured at a wavelength where Cu anomalous
> scattering is maximized (1.37 A). I'm thinking the problem is related to the
> wavelength used in data collection (refmac contains scattering factors and
> dispersion terms for Cu, Mo radiation.)
> CCP4 is using the proper Cu, Cl scattering factors (and anyway, if the
> contributions from these atoms were calculated as carbon the difference map
> peaks would be positive.) The temperature factors on the Cu, Cl, and
> non-disordered S atoms look fine.
> 
> When I refine with shelxl, the maps look normal, but the R factor isn't quite so
> good (0.17,
> 0.21). (The shelx faq says it also selects scattering factors for Cu, Mo, or Ag
> radiation, in this case it would also choose Cu radiation.) So, if the problem
> is related to scattering factors, wouldn't shelx show similar behavior?
> 
> Any ideas as to what I've missed and how to make refmac work?
> 
> Sue
> 
> --------------------------
> Sue Roberts
> Dept. of Biochemistry & Molecular Biophysics,
> University of Arizona
> suer@u.arizona.edu (520) 621-8171