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

Edward A. Berry BerryE at upstate.edu
Wed May 20 16:38:37 PDT 2015

Fe-Ligand bond lengths depend significantly on redox and spin
state of the iron (which drives the conformational change in
hemoglobin). Could it be the state of your iron is different from
what metal_coordination assumed in making the .edits file?

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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