Dear all First of all, thanks for the replies here and off-list. I reprocessed the data to 2 A, and modeled two copies of the ligand in each of the two protein NCS molecules, without using NCS restraints for refinement. I also calculated an SA omit map and a polder map. In the end, the ligand molecules have a relatively low B factor and CC of 0.8 and 0.9. The fact that these two ligands are in the same place (active site) in both NCS copies suggests they are not some random noise.
However, I also could model two more of the ligand outside of the active site, also with low B factor and CC > 0.8. Can I call these 'adventitious' molecules? Thanks. Mohamed On Thu, 23 Feb 2017 13:56:05 +0000, Mohamed Noor <mohamed.n...@staffmail.ul.ie> 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
