<div dir="ltr">Emily<div><br></div><div>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.</div><div><br></div><div><a href="http://www.phenix-online.org/newsletter/CCN_2015_01.pdf#page=6">http://www.phenix-online.org/newsletter/CCN_2015_01.pdf#page=6</a><br></div><div class="gmail_extra"><br></div><div class="gmail_extra"><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify">Tips for coordinated <span class="">metal</span> refinement<u></u><u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify">It is not uncommon to observe pronounced residual (difference) map features around <span class="">metal</span> ions. These features may originate from a number of possible reasons, such as: a) underrefined <span class="">metal</span> parameters, b) inoptimal <span class="">metal</span> parametrization, c) Fourier map artifacts, d) partial or/and shared occupancy, e) incorrect <span class="">metal</span> identity.<u></u><u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify">Provided that the <span class="">metal</span> identity is correctly assigned, refinement hints below may be helpful:<u></u><u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify">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:<u></u><u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px"><span style="font-size:8pt;font-family:Courier;background:silver">HETATM 3241 SN SN C 3 5.000 5.000 5.000 0.25 41.55 SN4+</span><span style="font-size:8pt;font-family:Courier"><u></u><u></u></span></p><p class="MsoNormal" style="font-size:12.8000001907349px"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify">2) Refine occupancy of the <span class="">metal</span>.<u></u><u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify">3) If it is a heavy <span class="">metal</span> (has substantially more electrons than typical macromolecular atoms C, O and N), refine anisotropic ADP of <span class="">metal</span>.<u></u><u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify">4) If it is anomalous scatterer refine f’ and f’’.<u></u><u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify">5) Run refinement until convergence. Usually it takes more than default 3 macro-cycles, about 5-10 macro-cycles.<u></u><u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px;text-align:justify"><u></u> <u></u></p><p class="MsoNormal" style="font-size:12.8000001907349px">If the residual map features are Fourier map artifacts then there isn’t much one can do about it.<br></p><div><br></div><div><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : <a href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a> Email : NWMoriarty@LBL.gov<br>Fax : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a> Web : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, May 20, 2015 at 4:38 PM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Fe-Ligand bond lengths depend significantly on redox and spin<br>
state of the iron (which drives the conformational change in<br>
hemoglobin). Could it be the state of your iron is different from<br>
what metal_coordination assumed in making the .edits file?<span><font color="#888888"><br>
eab</font></span><div><div><br>
<br>
On 05/20/2015 07:03 PM, Emilia C. Arturo (Emily) wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
I'm refining a model at 2.9 A, where four chains are in the ASU, and<br>
each active site has an iron with a few ligands; the configuration of<br>
this active site is the topic here.<br>
<br>
Currently the iron-ligand distances are not ideal (according to<br>
CheckMyMetal and the ideal distances generated by<br>
phenix.metal_coordination), but they are within a range observed<br>
previously for structures of truncated versions of this enzyme;<br>
furthermore, the more the metal-ligand distances change towards ideal<br>
distances, the more positive and negative density I observe in the<br>
Fo-Fc, so it appears that this deviation from the 'ideal' is supported<br>
by the data. However, when I use the 'Optimize X-ray/stereochemistry<br>
weights' option during refinement, the metal-ligand distances change<br>
(the metal appears to do most of the moving), getting closer to ideal,<br>
and this generates more positive and negative density in the Fo-Fc<br>
map). However, clearly it's nice that optimizing the<br>
X-ray/stereochemistry weights reduces R-free (and keeps the R-f/R-work<br>
ratio fine as well).<br>
<br>
So what is the most appropriate approach here, in order to keep the<br>
metal-ligand distances that best support the data, but still reap the<br>
benefits of the optimized stereochemistry weights?<br>
<br>
Some details of the structure and refinement are these:<br>
The iron in each of the four chains in the ASU is coordinated with<br>
atoms from two histidines, a glutamate, and a water (so four ligands<br>
per Fe) and there remains un-modeled density in the iterative build<br>
comp OMIT map used for modeling (because resolution is 2.9A and adding<br>
more water (which is my best guess, given what truncated structures at<br>
higher resolution show coordinating the Fe) does nothing to the Rf).<br>
I am working with an .edits file generated by<br>
phenix.metal_coordination. After some experimentation, I've left the<br>
sigma values (for Fe-O and Fe-N) at default values, and added a<br>
restraint for Fe-O (water), using an ideal distance of 2.3 and a sigma<br>
value of 0.1.<br>
<br>
Emily.<br>
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