[sharp-discuss] Re: [ccp4bb]: Heavy Atom Negative Density

[Edward A. Berry]

Just a thought- could sharp be generating Fo/Phic coefficients for an 
artificial "native" protein lacking the irons? I think it would do, 
if the iron sites were used as "heavy atoms" in phasing, and they are 
listed as sites in every compound/crystal. Still, I would only expect
zero density in that case, not minus 5 sigma, unless the occupancies 
in the reference crystal were badly overestimated.
Ed

Paul Hubbard wrote:
> 
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> Hello all,
> 
> I am having trouble trying to find out why I am getting negative density
> for Fo(phic) maps calculated in SHARP. I managed to pull out possible Fe
> sites from a residual map using the anomalous signal from the peak
> wavelength (phases taken from data using just 1 Fe in the previous
> round). The refined occupancies and B factors seem okay (~1.0 and 10.0),
> and the FOM is okay (~0.35 to 3.0A for acentric reflections) - but the
> denisty only looks good at -5 sigma.
> 
> This is from that 4Fe-4S MAD data I was having trouble with a few weeks
> ago. Are these classic symptoms of some error I may have done? Any
> suggestions gratefully appreciated.
> 
> Thanks
> 
> Paul
> 
> --
> Paul Hubbard
> Dept. of Biochemistry
> Medical College of Wisconsin
> Phone: 414-456 4305
> Fax: 414-456 6510
> URL: iris9.biochem.mcw.edu