Hi Johannes,
Thank you very much for your answer and explanations. Actually, in the first place I already refined against neutron data (without X-ray) until convergence and the results are quite good. However, water orientations (in which we are particularly interested) are not easily discernible in the maps since the knowledge about water oxygen positions from the X-ray data are not explicitly implemented during refinement. Hence, we collected room-temperature X-ray data from a deuterated crystal grown in the same drop as the crystal used for neutron diffraction experiments. With the combined XN-data, it is astonishing how the R-free of both X-ray and neutron data drop significantly (by 2% for the neutron part) and how well the data agree. To account for the longer X-D/H bond lengths in nuclear density maps, we used the respective restraints for neutron data (Settings --> Advanced --> Model interpretation --> Use the nuclear distances for X-H/D).
this is good to hear, and this demonstrates the power of using more data. The only issue here, as I mentioned before, is that in joint XN refinement we refine one single model against two data sets, while ideally it should be two models in order to account for genuine unique information that is contained in X-ray and neutron data. This will be addressed at some point.
Overall, I would really like to use the XN-refinement approach to improve the model in particular with respect to its water structure. Ultimately, we will anyhow deposit the neutron, X-ray and joint XN structures.
Sounds like a very good plan!
Is it not possible at all to achieve coinciding coordinates and identical ADPs when using X and N at the same time?
I afraid no, sorry. This is purely technical limitation of current implementation.
The only alternative that I have not already used and would further improve the water structure in the model would be what you describe under 3. From what I read about it, however, it will be difficult to generate restraints also for water oxygens for which it would be particularly important in our case. Or is this possible in addition to the dihedral restraints for the protein? Thanks a lot!
The reference model restraints are applied to macro-molecule only (not water). Pavel