Re: Residual density around iron

[Garib Murshudov <garib@yorvic.york.ac.uk>]

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>    I'm refining a protein (350 residues) containing a single iron in the
active
> site. Although the refinement is not yet finished, the electron density for
most
> of the protein looks reasonable, especially around the active site, except
> for the iron itself. There resides a significant sphere-shaped Fo-Fc peak
> _around_ the iron (ca. 5 sigma, certainly the highest difference density peak
> in the entire structure). The 2Fo-Fc is there as well, of course, and an
anomalous
> fourier map clearly showed that the Fe is in its proper place.
> Maybe I should mention that I calculated the map with XPLOR 3.851 using
> sigmaa-weighting. Replacing the iron by a heavier atom (e.g. Zn) didn't
reduce
> the Fo-Fc (just the temp. factor of the Zn increased) , and it won't make
> sense anyway since the protein (an oxidoreductase) should only be active with
an
> iron. I also included the correction for the anomalous effect although we
> collected the data at 0.95 A wavelength far from the Fe-edge.
> Can anyone give me a clue what could be the reason?
>

One reason could be partial occupancy of Fe.I would check B-value of Fe
and surrounding atoms Especially protein atoms as waters might have correlated
partial occupancy with Fe). But before doing it I would refine few cycles with
the programs which use second derivative matrix (SHLEXL, TNT, REFMAC,
RESTRAIN).
In principle in sufficently high resolution (usually higher than 2.0A) there
always will remain residual density around heavy atoms like Fe due to
significant anisotropic effect. But it usually is not spherical.

Garib

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Garib N. Murshudov, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 43 35 89, work:  +44 (1904) 43 25 65
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