Dear all I think I have a ligand (substrate) placed in the active site of my model correctly. The CC is 0.785, B factor of 60 A^2 which is roughly similar to the neighboring residues and there was no ligand in my search model*. The data extends to 2.2 A, although I think I can get something higher with manual processing**. How can I be really sure that it is the ligand that I think it is? And assuming you are a reviewer, what would you expect to see in a manuscript?
* The unliganded model was obtained by molecular replacement using a search model that did not have the ligand. I then used this model to simply do one cycle of rigid-body refinement and another one cycle of coordinate/ADP refinement. ** The data was auto-processed during data collection using xia2/XDS. I have a dozen of datasets so I am just taking the autoprocessed ones and see if my ligand is there. Thanks. Mohamed
