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Re: [ccp4bb]: Refining Ions - Mn+2 Vs Mg+2...
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> I am trying to incorporate ions into my model.
> We know from previous data that we have Mn+2 ions in our structure. Most of us
> in the lab who have tried to refine the ions as Mn+2 in CNS
> (as per CNS tutorial) find that the R-factor and R-free increase (as much as
> 1% sometimes) and have continued to refine them as waters.
> It's the same situation whether it's Mn+2 or Mn.
> However, when I tried to refine all my Mn+2 as Mg+2 (by mistake),
> I found that the program handles it nicely and that there is a nice drop in
> R-factor and R-free.
> So, I am currently refining Mn+2 as Mg+2.
> Is there any explanation to what might be going on ? Does something need to be
> done differently to refine them as Mn+2 ions.
> Any words of wisdom/advice/suggestions/criticisms ?
> Thanks very much,
> Rajeswari Edayathumangalam
> Dept. of Biochemistry & Molecular Biology
> Colorado State University
> Fort Collins, CO 80523 USA
I cant explain why you do or dont have Mn or Mg, but there is an easy
way to distinguish - look at the crossec plots of f" for the two elements
Mn has a reasonable anomalous signal in the wavelengths 1- 1.5A,
Mg is virtually non-existent.
If you do a Dano map with your model phases you should see both the S;
signal 0.2-0.5 over that range and any Mn as higher peaks.
Best wishes Eleanor
PS - if Mg refines and Mn does not the restraints are probably set
differently - check the geometry targets..