Dear Veronica, In this case I would remove the poorly defined residues. They make your model worse. Herman
-----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von V F Gesendet: Mittwoch, 11. Januar 2017 16:33 An: [email protected] Betreff: Re: [ccp4bb] To delete main chain or not 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.
