On Mon, 2011-03-14 at 18:32 -0400, Zhang yu wrote:
I am working on a DNA-protein complex, the protein apo structure is already known. Recently I got a dataset of the DNA-protein complex, I tried to find a solution by autoMR in Phenix with the known protein coordinate as template. I got only one solution with very negative LLG (around -4000), and after rigid body refinement, the both Rwork and Rfree is around 0.55. Was there anyone in the same situation as me? What does that mean if there is just one solution while with very high negative LLG?
Could mean several things, but one thing is for sure - R~55% suggests that molecular replacement did not work. One possibility is that your protein undergoes conformational change when it binds to DNA. If it has distinct domains, you may be able to get a solution if running them as separate models. Negative LLG could mean that you did not correctly guess the unit cell content. Or maybe the space group is wrong. You may want to post the phaser log-file, since it's not obvious to me what you mean by only one solution. What were the Z-scores at rotation/translation steps? -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs