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 http://person.au.dk/da/[EMAIL PROTECTED] Tel. +45 8942 5025, Fax +45 8612 3178, [EMAIL PROTECTED]
