Hi all,

I apologise in advance for the long post. I am working on solving a structure that looks like it could have a ligand bound in the active site. My data was obtained from a crystal of just the soluble domain of my protein that had been soaked overnight in the ligand solution. The apo crystal structure is already known and so I have solved my structure using phaser MR. I have attached the Aimless report output of my structure at the end of this email. The current R values I have after refinement and adding in all the waters are Rfree: 0.2413 and Rwork: 0.1897. I can clearly see green density that is much larger (only disappears when I contour the Fo-Fc map to about 6 A) than in my control crystal that had been soaked in the same concentration of just solvent (I had used DMF).

I am struggling to add in my ligand as it doesn't seem like the entire ligand can fit in the green density. We think it may be because we have only used the soluble domain and so the ligand isn't held very securely since the transmembrane domain is missing. I have been trying to fit in smaller sections of it and doing an occupancy refinement. So far I have been able to get part of the ligand in with an occupancy of about 0.6 but after the refinement run, phenix.refine seems to move this part of the ligand slightly out of the area where I had tried to fit it into the green density. Interestingly, there isn't a big red density in the area that this ligand section has moved to. I would appreciate any advice on how I should proceed with trying to figure out if I have tried the correct section of the ligand and the kind of refinement settings to use with a weak binder.