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Well - I certainly would do more refinement - if something is bound there will be other changes in solvent etc. then search the difference map for peaks/ find ligand etc, and see what it shows.. If your original model and this one are isomorphous you can also check the Fobs-lig -Fobs-nolig Phi-nolig but that may not be necessary eleanor On 23 February 2017 at 13:56, Mohamed Noor <[log in to unmask]> wrote: > 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 >