[phenixbb] metal-ligand distances, and Optimize X-ray/stereochemistry weights

Edward A. Berry BerryE at upstate.edu
Thu May 21 11:42:43 PDT 2015

Well - I'm not an expert on the programs or on coordination chemistry -
I just know the problem exists. Perhaps others can help out here.
I would try setting a rather large sigma value and perhaps a few pm of slack
for these bond lengths in the .edits file. That down-weights or unweights the
restraints for these bonds where the ideal values are uncertain.
Then re-optimize overall weights and see if you get the same improvement
without disturbing the iron coordination.  anisotropic ADP refinement
sounds like a good idea.

His Ne2 - Fe distances in cytochromes tend to be right around 2.0 A.
there are structures of cyt c that purport to be in oxidized and
reduced states, but this may have been before the reducing effect
of radiation was recognized -maybe both are reduced.
His - Fe in Oxyhemoglobin  is around 2.0 A (1.94 in 1hho), increasing
by about 0.1 A in deoxy to as much as 2.15 A. For Fe - carboxylate
you could look at feroxidase site in bacterioferritins, don't know
if there are any really high resolution structures.

On 05/21/2015 02:10 PM, Emilia C. Arturo (Emily) wrote:
>  > Could it be the state of your iron is different from
>  > what metal_coordination assumed in making the .edits file?
> Yes, you're absolutely right, and I hadn't found documentation for phenix.metal_coordination to help me gauge whether 'my' irons were like those used to inform how phenix generated the edits file. Do you happen to know on what the tool bases its ideal distances?
> Do you have any references you can share that discuss how Fe-ligand distances change with charge and spin state, whether its observable in crystal structures or solution? Or, maybe you can suggest search terms to help me out as I am quite naive about bio-inorganic chemistry?
> Emily.
>  > eab
>  >
>  >
>  > On 05/20/2015 07:03 PM, Emilia C. Arturo (Emily) wrote:
>  >>
>  >> I'm refining a model at 2.9 A, where four chains are in the ASU, and
>  >> each active site has an iron with a few ligands; the configuration of
>  >> this active site is the topic here.
>  >>
>  >> Currently the iron-ligand distances are not ideal (according to
>  >> CheckMyMetal and the ideal distances generated by
>  >> phenix.metal_coordination), but they are within a range observed
>  >> previously for structures of truncated versions of this enzyme;
>  >> furthermore, the more the metal-ligand distances change towards ideal
>  >> distances, the more positive and negative density I observe in the
>  >> Fo-Fc, so it appears that this deviation from the 'ideal' is supported
>  >> by the data. However, when I use the 'Optimize X-ray/stereochemistry
>  >> weights' option during refinement, the metal-ligand distances change
>  >> (the metal appears to do most of the moving), getting closer to ideal,
>  >> and this generates more positive and negative density in the Fo-Fc
>  >> map). However, clearly it's nice that optimizing the
>  >> X-ray/stereochemistry weights reduces R-free (and keeps the R-f/R-work
>  >> ratio fine as well).
>  >>
>  >> So what is the most appropriate approach here, in order to keep the
>  >> metal-ligand distances that best support the data, but still reap the
>  >> benefits of the optimized stereochemistry weights?
>  >>
>  >> Some details of the structure and refinement are these:
>  >> The iron in each of the four chains in the ASU is coordinated with
>  >> atoms from two histidines, a glutamate, and a water (so four ligands
>  >> per Fe) and there remains un-modeled density in the iterative build
>  >> comp OMIT map used for modeling (because resolution is 2.9A and adding
>  >> more water (which is my best guess, given what truncated structures at
>  >> higher resolution show coordinating the Fe) does nothing to the Rf).
>  >> I am working with an .edits file generated by
>  >> phenix.metal_coordination. After some experimentation, I've left the
>  >> sigma values (for Fe-O and Fe-N) at default values, and added a
>  >> restraint for Fe-O (water), using an ideal distance of 2.3 and a sigma
>  >> value of 0.1.
>  >>
>  >> Emily.
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>  >

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