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On Aug 3 2006, Yi Xue wrote:
I have one dataset, diffracted to 3.2A.
It should be a protein-DNA complex. The protein structure has already
been solved. The DNA is a 23mer.
I used phaser to do the molecular replacement, and it found a
solution, RFZ=7.2, TFZ=11.9, however, LLG is negative.
You've already had good advice to look for density for DNA, probably
preferably before any refinement. I'd just add to this that if you have a
negative LLG score, this implies that the model is not as good or as
complete as you have told Phaser that it is. You should check that Phaser
has used a sensible estimate for the RMS error of the model, and also that
you have specified the COMPOSITION correctly. One very common error is to
specify the composition of the search model, but what Phaser needs to know
is the composition of the asymmetric unit, whether you have a complete
model for everything in there or not!
Randy Read
