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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