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

Nigel Moriarty nwmoriarty at lbl.gov
Wed May 20 17:33:43 PDT 2015


The ideal value in your .edits file may not be what is the correct value
for your situation. You should feel free to adjust the ideal value as you
see fit to improve the fit to the density. I have also included some other
metal fitting tips from Comput. Cryst. Newsl.


Tips for coordinated metal refinement

It is not uncommon to observe pronounced residual (difference) map features
around metal ions. These features may originate from a number of possible
reasons, such as: a) underrefined metal parameters, b) inoptimal metal
c) Fourier map artifacts, d) partial or/and shared occupancy, e) incorrect
metal identity.

Provided that the metal identity is correctly assigned, refinement hints
below may be helpful:

1) Ensure charge is in the model input file. In case of PDB file it is
defined in rightmost part of ATOM record, for example:

HETATM 3241  SN   SN C   3       5.000   5.000   5.000  0.25
41.55          SN4+

2) Refine occupancy of the metal.

3) If it is a heavy metal (has substantially more electrons than typical
macromolecular atoms C,  O and N), refine anisotropic ADP of metal.

4) If it is anomalous scatterer refine f’ and f’’.

5) Run refinement until convergence. Usually it takes more than default 3
macro-cycles, about 5-10 macro-cycles.

If the residual map features are Fourier map artifacts then there isn’t
much one can do about it.



Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Wed, May 20, 2015 at 4:38 PM, Edward A. Berry <BerryE at upstate.edu> wrote:

> 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?
> 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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