Dear all, Recently I crystallized and solved the structure of a protein using molecular replacement. The crystal diffracts to 1.8A and has the R free of 0.21. During refmac and phenix refinement, I found that the N-terminal (~25 amino acids) electron density wasn't quite good, especially a proline residue. It not only has little side chain electron density, but also doesn't have continuous electron density between backbone C-N until the sigma level going down until 1.2. A normal backbone sigma contour level is above 2.5 in this structure. I calculated composite omit map as well as the difference map. In addition, NCS maps of those were calculated. But its density is still unclear. As proline normally has rigid structure and good electron density, will this mean some potential mistake in the structure?
There seems no other way to trace the backbone. And the upstream and downstream residues are not that bad. If no way to find the solution, could there be an explanation about the poor electron density of protein. By the way, this proline is connecting a beta-sheet and an alpha-helix, which is on the surface of the protein. Also, the protein is soluble and has about 300 amino acids. You kind suggestions will be greatly appreciated! Dolphin
