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Solution structure of a c-JUN 5' UTR stem-loop associated with specialized cap-dependent translation initiation
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1.0 mM RNA 100% D2O 20mM Sodium Phosphate 6.1 1 atm 298 Bruker AVANCE III 800 2 2D 1H-1H NOESY 1.0 mM RNA 90% H2O/10% D2O 20mM Sodium Phosphate 6.1 1 atm 278 Bruker AVANCE III 800 3 2D 1H-1H NOESY 1.0 mM [A,G-98% D3',4',5',5"; C,U-98%: D3',4',5, 5',5"] RNA 100% D2O 20mM Sodium Phosphate 6.1 1 atm 298 Bruker AVANCE III 800 4 3D 1H-13C NOESY 1.0 mM [A,C,G,U-98% 13C, A,C,G,U-98% 15N] RNA 100% D2O 20mM Sodium Phosphate 6.1 1 atm 298 Bruker AVANCE III 800 5 2D 1H-15N HSQC 1.0 mM [A,C,G,U-98% 13C, A,C,G,U-98% 15N] RNA 90% H2O/10% D2O 20mM Sodium Phosphate 6.1 1 atm 278 Bruker AVANCE II 600 6 2D 1H-13C HSQC 1.0 mM [A,C,G,U-98% 13C, A,C,G,U-98% 15N] RNA 100% D2O 20mM Sodium Phosphate 6.1 1 atm 298 Bruker AVANCE III 800 7 2D 1H-1H TOCSY 1.0 mM RNA 100% D2O 20mM Sodium Phosphate 6.1 1 atm 298 Bruker AVANCE III 800
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 800 2 Bruker AVANCE II 600
NMR Refinement Method Details Software simulated annealing X-PLOR NIH
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 200 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 3 collection TopSpin Bruker Biospin 4 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 5 peak picking Sparky Goddard 6 peak picking CcpNmr Analysis CCPN 1 structure calculation X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 2 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 7 chemical shift assignment TopSpin Bruker Biospin