Just echoing what has been said. I would make sure you have the right space group. It may be worthwhile tyring to find a MR solution in different space groups with different compositions. Another imporatant thing is how complete is your model? Do you have all the protein and DNA modeled in? How many waters (you should see plenty at 1.5 A) How good is the difference map? These are all things that should be checked before panic sets in....
Cheers
