Abstract
We compiled an NMR data set consisting of exact nuclear Overhauser enhancement (eNOE) distance limits, residual dipolar couplings (RDCs) and scalar (J) couplings for GB3, which forms one of the largest and most diverse data set for structural characterization of a protein to date. All data have small experimental errors, which are carefully estimated. We use the data in the research article Vogeli et al., 2015, Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics, J. Struct. Biol., 191, 3, 306–317, doi:10.1016/j.jsb.2015.07.008 [1] for cross-validation in multiple-state structural ensemble calculation. We advocate this set to be an ideal test case for molecular dynamics simulations and structure calculations.
Highlights
Compiled data set of exact NOE distance limits, residual dipolar couplings and scalar couplings for the protein GB3
Previous input distance restraints were scaled by a factor of 3 1/6 1⁄4 0.83268 per methyl group such that the corresponding cross-relaxation rate constant is a sum over all individual contributions
This would be strictly true if the methyl motion was slow
Summary
350–500 ml of 2–4 mM protein solution in 97%/3% or 95%/5% H2O/D2O, 50 mM potassium phosphate buffer, pH 6.5–7.0, and 0.5 mg/ml sodium azide. Previous input distance restraints were scaled by a factor of 3 1/6 1⁄4 0.83268 per methyl group such that the corresponding cross-relaxation rate constant is a sum over all individual contributions. This would be strictly true if the methyl motion was slow (slower than nanoseconds). The apparent crossrelaxation rate constants were fitted to the same formulae as used for single atoms or methyl groups, corrected for spin diffusion [4] and normalized to the equivalent of a superposition of contributions from all pairs of single atoms.
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