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An old example:
The Phe-tRNA:EF-Tu:GDPNP ternary complex - three complexes per asymmetric
unit, C2 space group, degenerate three-fold NCS (three different tRNA
conformations in the trimer). 40 - 2.8 Å resolution native data (about 78%
complete...) used for MR. Straight-forward placement of three EF-Tu copies
using 10 - 3.5 Å resolution data (AMORE).
A single copy of a truncated tRNA model (representing about 7% of the
macromolecular mass of the asymmetric unit) was placed using data in the
15 - 6 Å range (AMORE) and identified by significantly better statistics
of the corresponding TF solution (with EF-Tu molecules placed as prior
models) compared to all other RF solutions - ~48% R-factor compared to
~52%+ for other solutions as I recall, and similar distinction of PC
value. Optimisation of the RF peak value for this single solution (by
variations of RF search parameters) produced a second solution in the RF
top-100 peak list that also yielded a distinct solution in TF. Third tRNA
molecule was placed by screening of the degenerate three-fold rotation by
"manual" MR. Only low resolution data worked for the tRNA MR.
Gradual model refinement (TNT) completed the structure (PDB 1TTT) and
bogus occupancy refinement of tRNA complemented B-factor refinement as
judged by a significantly improved Rfree value. Post-refinement using CNS
with proper ML target and anisotropic scaling makes the bogus occupancy
refinement obsolete - today TLS parameterisation would probably do an even
better job).
I didn't check but the tRNA RMSD (truncated model vs. refined structure)
will probably exceed 1 Å.
All pretty well decribed in:
Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF,
Nyborg J (1995). "Crystal structure of the ternary complex of Phe-tRNAPhe,
EF-Tu, and a GTP analog.” Science, 270, 1464-72.
Poul
> would anyone be willing to share stories of the worst molecular
> replacement search probes they used to get the correct solution purely
> with MR?
>
> perhaps in terms of %-scattering, RMSD, Z-score, LLG, or other possibly
> specific scoring values.
>
> -bryan
>
>
--
========================================================
Poul Nissen, professor, ph.d.
Centre for Membrane Pumps in Cells and Disease - PUMPKIN
University of Aarhus, Dept. Molecular Biology
Gustav Wieds Vej 10C, DK - 8000 Aarhus C, Denmark
http://www.mb.au.dk
http://www.bioxray.dk
http://www.pumpkin.au.dk
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Tel. +45 8942 5025, Fax +45 8612 3178, [log in to unmask]
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