The degree of coupling between these two distal sites is small (|ρ|≈0.1), but the correlations are statistically significant (P<0.00001) and agree with those observed in the conformational ensemble determined for ubiquitin from NMR data21.
With a sufficiently large ensemble (determined through experimentation), the mean state should represent the maximum likelihood value for the process at the time.
This fidelity is calculated for a post-selected ensemble determined by the signal (s tau)), which is a weighted integral of the measurement record: s tau) = int_{0}^{tau} f(t) j t),dt.
Using synthetic data we find that an ensemble that has been determined by ensemble-refinement is more similar to a reference ensemble than an ensemble determined using standard single-molecule refinement.
This plot clearly shows that at all dimensions the ensemble
The strength of the backbone correlation associated with this motion (ρ≈−0.6) was found to be similar to that derived from conformational ensembles determined with20 and without8 restraints derived from experimental NMR parameters.
Generally, the structural ensembles determined using autoNOE-Rosetta are closer to the nearest PDB reference structures by approximately 0.5 Å for RTT, 0.2 Å for ms6282, 0.5 Å for aLP and >2.2 Å for nEIt relative to the structures predicted by CYANA (Supplementary Figure 14).
We first calculated the harmonic ensemble similarity between the reference ensemble and the ensembles
To obtain a more detailed view that includes both atoms in the polypeptide backbone chain and in the side chains we proceeded to calculated the pairwise all-atom (excluding hydrogens) RMSD between all 2307 conformations (reference ensemble and five ensembles determined using NOE restraints).
DOI: http://dx.doi.org/10.7554/eLife.02777.007 10.7554/eLiFigure77.008 Figure 1 figure supplement 5. Validation of the RDC-refined structural ensembles determined in this work representing the free and triNAG-bound states of human lysozyme.
The size of the null ensemble is determined by the input choice of using either the fixed or adaptive ensemble size (see Section 4.5).
