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:[log in to unmask]] Im Auftrag von V F
Gesendet: Mittwoch, 11. Januar 2017 16:33
An: [log in to unmask]
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.
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