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NMR solution structure of the exon/intron binding site 1 (EBS1/IBS1) of the group II intron Sc.ai5(gamma)
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA 100% D2O 100 6.3 ambient 288 2 2D 1H-1H NOESY 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA 100% D2O 100 6.3 ambient 293 3 2D 1H-1H NOESY 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA 100% D2O 100 6.3 ambient 298 4 2D 1H-1H TOCSY 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA 100% D2O 100 6.3 ambient 288 5 2D 1H-1H TOCSY 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA 100% D2O 100 6.3 ambient 293 6 2D 1H-1H TOCSY 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA 100% D2O 100 6.3 ambient 298 7 2D 1H-1H NOESY 0.9 mM RNA (7A-MER), 0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA 90% H2O/10% D2O 100 6.3 ambient 278 8 2D 1H-13C HSQC 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA 100% D2O 100 6.3 ambient 288
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 700
NMR Refinement Method Details Software torsion angle dynamics, simulated annealing TopSpin
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 200 Conformers Submitted Total Number 20 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 processing TopSpin 1.3, 2.0, 2.1 Bruker Biospin 2 chemical shift assignment Sparky 3.1 Goddard 3 data analysis Sparky 3.1 Goddard 4 peak picking Sparky 3.1 Goddard 5 structure solution DYANA 1.5 Guntert, Braun and Wuthrich 6 structure solution CNSSOLVE 1.2 Brunger, Adams, Clore, Gros, Nilges and Read 7 refinement X-PLOR NIH 2.16 Schwieters, Kuszewski, Tjandra and Clore