Dear Herman and Pavel, > > First a remark: the pdb is a repository and if you insist, they will accept > anything you send them so, yes you can deposit this. > However, your question is off course, do I want to deposit this? One does not > want to end up in the twilight gallery or > deposit a structure where other crystallographers make fun of.
Hope I can avoid this! > If you want to keep the residues, you need help from your free Rfactor. You > need to refine as good as possible the R/Rfree is about 22/26. Whether, if I remove some of the residues (4-5), it drops by about 0.5 %. > > Since you mention that the disorder only occurs when a ligand is bound, it > might have a (biological) function, which would provide an incentive to > delete the poorly defined regions to illustrate this. However, if you > obtained your ligand complex by soaking, the disorder might be caused by the > fact that an interesting conformational change is blocked by the crystal > packing. In this case you should try to get the complex by cocrystallization > as well, otherwise you might have to do this when you receive the referee > reports of your paper. > > models refined against low-resolution data (diffraction or cryo-EM) should > have zero geometry violations (such as Ramachandran plot outliers or rotamer > outliers). This does not mean real structures do not have such violations > (in fact they do and there plenty of examples), but low-res data can't > justify them. Thank you.
