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The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/3'GGAU
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-1, 80 mM sodium chloride-2, 10 mM sodium phosphate-3, 0.5 mM EDTA-4 90% H2O/10% D2O 0.1 6.1 ambient 274 2 2D 1H-13C HSQC 1 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-1, 80 mM sodium chloride-2, 10 mM sodium phosphate-3, 0.5 mM EDTA-4 90% H2O/10% D2O 0.1 6.1 ambient 274 3 2D 1H-1H TOCSY 1 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8 100% D2O 0.1 6.1 ambient 274 4 2D DQF-COSY 1 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8 100% D2O 0.1 6.1 ambient 274 5 2D 1H-31P HETCOR 1 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8 100% D2O 0.1 6.1 ambient 274 6 2D 1H-1H NOESY 1 mM RNA (5'-R(*GP*GP*UP*AP*GP*GP*CP*CP*A)-3')-5, 80 mM sodium chloride-6, 10 mM sodium phosphate-7, 0.5 mM EDTA-8 100% D2O 0.1 6.1 ambient 274
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 600 2 Varian INOVA 500
NMR Refinement Method Details Software simulated annealing Sparky
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 40 Conformers Submitted Total Number 10 Representative Model 1 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment Sparky 3.12 Goddard 2 data analysis Sparky 3.12 Goddard 3 collection VNMR 6.1C Varian 4 structure solution CNS 1.2 Brunger, Adams, Clore, Gros, Nilges and Read 5 refinement Amber 9 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm