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Re: [ccp4bb]: Can I find a zinc in a haystack?
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On Thu, 25 May 2000, Pawel Grochulski wrote:
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> > Depends upon the quality of the crystal and your data quality and
> > redundancy. We are able to easily measure anomalous differences at the
> > Fe K-edge for a protein of similar size (soybean L-1 lipoxygenase, 94 kDa,
> > typical diffraction to 1.6 angstroms), so I wouldn't hesitate to try.
> > Diana
> Hi Diana,
> The Bijvoet signal can be estimated from
> the formula:
> sqrt(1/2)sqrt(Na/Np)(2f''/Zef) where:
> Na - number of Zn(Fe) atoms per protein molecule
> Np - number of non-H atoms in the protein molecule
> Zef - average atomic number in proteins (~6.7)
> Assuming ~94kD protein (about 7015 non-H atoms) and one Fe atom (f''~3.9)
> the signal will be at the level of ~1%, unless the f'' at peak is much
> higher due to the presence of the "white lines", but this is usually
> observed at the L edges.
> I wonder how strong was your Bijvoet signal and if this would be enough
> to solve your structure doing MAD at the Fe K-edge?
I can refer you to a literature citation (Biochemistry vol. 32, pp.
6320-6323, 1993), which shows an anomalous difference map for this
protein calculated from data collected on a home rotating anode source.
The data used to calculate the map was from 30 - 6 angstroms, and the
Fe peak was the highest peak in the map, at 5.8 times the map rms
density. Recently we collected data at the APS on this protein at the
Fe edge, but due to unfortunate circumstances it was quite incomplete,
so I am reluctant to quote any statistics from this data set, except
to say that preliminary data processing and scaling in HKL2000 indicated
a reasonably strong anomalous signal. Since the original posting asked
whether one could use the anomalous signal from one Zn atom at the K-edge
of Zn to verify a molecular replacement solution, I stand by my original
Could one use this signal to solve our structure via MAD at the Fe
K-edge? This would be an interesting experiment that I'm sure will be
tried in the future.
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Diana R. Tomchick
Department of Molecular Physiology and Biological Physics
Rm. 4223, Jordan Hall
University of Virginia
1300 Jefferson Park Avenue
Charlottesville, VA 22908