RE: [ccp4bb]: Mn versus Mg..Continues

[paula <paula@strubi.ox.ac.uk>]

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Hi, Raji.

I have Mn in my structure and also Mg in other complexes. I never had a 
problem with CNS not refining Mn properly, so may be, as Eleanor suggested 
your restrains for Mn are not properly set. to distimguish between Mn and Mg I 
calculate an anomalous difference Fourier map - depending on your wavelenght, 
Mn should have a very high peak and Mg should have a peak weaker than S.

About your question on ligands, in CNS, when you do minimize refinement 
(minimize.inp), you can set a particular group of atoms as fixed - see "atom 
selection" - and refine evrything else. Then, when refining the B-factors 
(bindividual.inp), you set it to refine the Bs for all atoms. This should keep 
your ligand in its original position, refine everything else and then refine 
the B factors for all your atoms.

Hope this helped.

Paula Salgado

>===== Original Message From raji <raji@lamar.colostate.edu> =====
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>
>Hi All,
>Thanks to everyone who already replied my email.
>All prior work done by my PI and all other structures from our lab have
>reported these ions as Mn.
>Recent publications from another lab have shown unambiguously that these ions
>are indeed Mn+2. Here's the paper:
>Proc Natl Acad Sci U S A  2002 Aug 20;99(17):11169-74
>DNA-dependent divalent cation binding in the nucleosome core particle.
>Davey CA, Richmond TJ.
>The authors identified the ions as Mn2+ ions by calculation of a difference
>Fourier map by using anomalous dispersion differences for structure factor
>amplitudes and phases corresponding to the refined atomic model lacking metal
>ions. In addition, these ions are bound with very high occupancies.
>I am fairly convinced the DNA-bound ions are Mn+2.
>Also, we DO NOT have Mg in our buffers.
>I ended up refining them as Mg by MISTAKE one time instead of writing them as
>Mn and that's when I noticed that CNS seemed to handling it better as Mg.
>Im still not clear about what's going on.
>Why would putting in Mg help Rfac & Rfree, if the # electrons Mg = # 
electrons
>Water ?
>Could someone pl. share your thoughts.
>Thanks for your immediate responses.
>Raji
>
>Rajeswari Edayathumangalam
>Dept. of Biochemistry & Molecular Biology
>Colorado State University
>Fort Collins, CO 80523 USA