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RE: [ccp4bb]: MR + SIR



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James -

Since you have 4 copies/asu, have you considered applying NCS to average
your maps?
I have used SIR+averaging previously (see DeLaBarre et al, NSB Feb? 2000) to
distinguish proper handedness and bootstrap my way into model building.

Byron DeLaBarre

> -----Original Message-----
> From: owner-ccp4bb@dl.ac.uk [mailto:owner-ccp4bb@dl.ac.uk]On Behalf Of
> James Stroud
> Sent: Saturday, July 06, 2002 8:47 PM
> To: ccp4bb@dl.ac.uk
> Subject: [ccp4bb]: MR + SIR
>
>
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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> 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
>
> --------------------------------------------------------
> "Research: If it worked the first time,
> they would just call it 'search'."     -Roy Garcia
> --------------------------------------------------------
>  James C. Stroud
>  Department of Chemistry and Biochemistry
>  University of Colorado at Boulder
>  Boulder, CO 80309
>
>  Tel: 303-492-4503      Fax: 303-735-1347
> --------------------------------------------------------
>