There are certainly reasons why it shouldn't work: - the protein may alter the structure - even if its not a "big bender", it may tweak the groove widths or introduce a shallow overall bend in a long binding site - the phosphates move the most between DNA structures, and unfortunately they also scatter the most.
That said, it really can work! My student got very nice results using phaser and model-built 5-bp chunks of duplex DNA. Using short chunks avoided the problem of an unknown overall bend. It didn't find everything, but it certainly helped us get a toehold on the phase problem. So go for it. Phoebe ---- Original message ---- >Date: Fri, 5 Dec 2008 16:32:14 -0600 >From: UT MDACC <[EMAIL PROTECTED]> >Subject: [ccp4bb] MR with DNA >To: CCP4BB@JISCMAIL.AC.UK > >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 Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
