[phenixbb] Molybdenum cofactor refinement

Pavel Afonine pafonine at lbl.gov
Wed Nov 20 10:57:41 PST 2019

Hi Cristiano,

if Molybdenum site isn't disordered, it should have a very prominent 
peak at 1.9A resolution, which in turn means metal coordination 
restraints may not be necessary. So have you tried to refine without 
these restraints?

You may try to refined occupancy of Mo in case it is partially occupied. 
Also, it's heavy enough to warrant refinement of its anisotropic ADP.

Finally, clashes may also be false alarms because Molprobity clash 
evaluators are unaware of non-standard geometries and bonds.

I can have a closer look if you send me files (off mailing list).


On 11/20/19 07:24, Cristiano Mota wrote:
> Hi all,
> I'm using phenix.refine to refine a structure of a Molybo-protein at 1.9Å.
> The MGD cofactors (molybdopterin guanine dinucleotide) are being 
> refined with a weird distorted geometry causing some clashes. The 
> Fo-Fc maps show that something is going wrong in the aromatic rings 
> interatomic distances.
> I'm using the readyset to pick up MGD and metal restraints.
> Am I using the right protocol?
> Best regards,
> Cristiano Mota

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