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[ccp4bb]: MR + SIR
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I am working on a protein-dna complex and have crystals that diffract to
about 3.2. I believe I have enough information to solve the structure but I
am racking my brain as to how to attack the problem. It seems that I am in
P2(1) and my DNA is making a pseudo-continuous helix along the y-axis. It is
a 15mer so it naturally generates the screw. From MR and also from my
(presumably) finding most of the sites in the SIR derivative, it appears
that the DNA is lining up right on all of the symmetry elements. So I have 4
complexes per ASU. The problem is that P2(1) is a polar space group so each
MR solution seems to have an arbitrary y position with respect to the
others. Thus, I can not improve my MR phases by using a combination of
solutions from MR. I have naively tried this before realizing my error. My
derivative is iodinated DNA (5 position of thymine). There are two reasons I
am having a problem using the iodinated sites to "fix" the dna. First, there
is ambiguity in which way it runs as both directions can produce the same
pattern. Second, is the handedness issue of SIR. These phases are not strong
enough to determine by visual inspection whether the DNA is of the proper
handedness. I have tried to fix one MR solution and find others, but both
cns and molrep gave ridiculous solutions wherein the DNA was packing with
DNA and/or two complexes significantly overlapped. No matter what I do, I
can't see my protein in any map, which would help tremendously. Given that
the cell dimensions are huge (101 95 113), I don't believe it is a dna only
crystal. I am looking at other derivatives, but in the meantime, I would
like to try to solve this computationally. Does anyone know what ccp4 or
other programs could help with this or am I overlooking something obvious in
my approach to MR?
James
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"Research: If it worked the first time,
they would just call it 'search'." -Roy Garcia
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James C. Stroud
Department of Chemistry and Biochemistry
University of Colorado at Boulder
Boulder, CO 80309
Tel: 303-492-4503 Fax: 303-735-1347
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