In addition to the possible problem Ho mentioned (DNA conformational changes), a few other things could effect how doable it is: percentage of DNA vs protein in the complex and the resolution of the data. Too little DNA mass wouldn't help phase the remainder of the complex, if it could be located. Too low resolution and the completeness of the model gets worse for phasing (but too high resolution and you might run into issues with slight changes in DNA conformation causing problems searching). You might also want to look into Bill Scott's paper where he was doing MR on an RNA molecule using small RNA stretches (I don't have the reference at the moment).
Pete UT MDACC wrote: > Is there any existing example about anybody trying to do molecular > replacement for a protein-DNA complex using any B-DNA from the pdb database. > I am wondering 1) whether it is doable 2)if it is not doable, why not? > Thanks in advance for the feedback
