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[ccp4bb]: Summary: Atoms used for anomalous dispersion

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Dear All

Thanks to the many of you who responded to my question about the current
usage of heavy atoms
for solving structures using MAD. FYI, here is a summary of what I received

It seems that there hasn't really been a comprehensive review of this for
some time now. Pete Dunten
pointed me to an article in Synchrotron Radiation News Vol 8 No 3, pp 13-18
(1995)  written by Craig
Ogata & Wayne Hendrickson, and Manfred Weiss referenced a later article from
1999 also by Wayne
Hendrickson (J. Synchrotron Rad. 6, 845-851).

Pierre Rizkallah said that he and his colleagues had found Xenon at high
pressure to be an excellent
choice, their results for this work on the structure of  crustacyanin will
appear very soon in Acta D.
(Cianci et al). Pierre also reminded me that sulphur (sulfur if you
celebrate July 4th) has a useful
anomalous signal at around 2.0 A and he will also be publishing work using
this method in a
forthcoming paper.

Mischa Machius made the comment that 3 wavelength experiments are often
unnecessary and that
the anomalous signal from a single atom of e.g. iron or zinc per protein
molecule can be enough for
structure determination with MAD. He also advocated the use of elements that
have a significant
anomalous signal close to the copper K-alpha wavelength and therefore do not
require a trip to the
synchrotron. Even mercury, he points out, has 7.7 anomalous electrons at
1.54 A and suggested that
we might possibly have been able to solve our PDZ structure in-house. He and
his colleagues just
solved a protein using Xenon at 1.54 A, with 4 atoms per 47 kDa molecule
(another plug for Xe there).

Nukri Sanishvili listed a whole slew of elements (Fe, Co, Zn, Se, Br, Rb,
Ta, W, Re, Os, Ir, Pt, Au, Hg,
Tl, Pb, U) with which they have had success on the beamline I9ID at the APS
(Argonne Il.) and points
out that Se-Met has become a very popular choice due to the very high
success rate that it has for
phasing. As Nukri says, the number of Se atoms generally increases with the
size of the protein and there
is no disturbance of the crystals by soaking as is required for traditional
heavy-atom labeling.

My own experience with Se-Met has led me to ...


  "The probability of a methionine residue occurring in a protein is
    proportional to my desire to solve the structure of that protein"

  "The probability of finding a methionine residue at any given point in my
protein is
   directly proportional to the conformational flexibility of my protein at
that point"

Please don't flame me or bombard me with your "selenomethionine has changed
my life" stories, I know
it works very well, but I just haven't been very lucky with it so far !

Jan Abendroth also put me onto the articles that I have already cited, as
well as mentioning a third,
C. Ogata (1998)  "MAD phasing grows up" Nat Struct Biol Synchrotron suppl,

Bill Hunter told me that he and his colleagues did a survey of the elements
used for MAD a few years ago
(did you publish the survey Bill?) and also cited many of the elements that
Nukri's list contained.

Allen Matte made the excellent suggestion of having specific phasing records
included in the PDB database
format. This would make the compilation of the kind of statistics that I was
after, effectively automatic, since
users would be able to compile their own surveys directly from the database
itself. How about it RCSB?

Ana Gonzalez pointed out that you can do MAD with any element that has an
absorption edge within the
energy range of the most commonly used beamlines (7000 - 15000 eV) and that
L edges like the one that
we used in our PDZ structure determination, often give better results than K
edges. Along with mercury, she
also recommended gold and lead as good candidates, expressed reservations
about using platinum
which she says tends to yield many poorly occupied sites and a resulting
poor signal, and also recommended
Lanthanides for their excellent signal with the caveat that they may be
harder to get to bind to your protein
(apparently they substitute for Ca very well in Ca binding proteins).
Tantalum bromide has been used for very
large cells (didn't they use this for the ribosome?) and Ana also concurred
with the recommendation for trying
high pressure derivatization using Xe and NaBr.

With sincere apologies to anybody I might have missed out and my thanks to
all who replied.