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NMR structure of the III-IV-V three-way junction from the VS ribozyme
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 1D flip-back watergate 1H 1.5-2.0 mM [U-100% 15N] J345-1-1, 5mM MgCl2 90% H2O/10% D2O 55 6.5 288 2 2D 1H-15N HSQC 1.5-2.0 mM [U-100% 15N] J345-1-1, 5mM MgCl2 90% H2O/10% D2O 55 6.5 288 3 2D 1H-15N HSQC NH2 only 1.5-2.0 mM [U-100% 15N] J345-1-1, 5mM MgCl2 90% H2O/10% D2O 55 6.5 288 4 3D 1H-15N NOESY 1.5-2.0 mM [U-100% 15N] J345-1-1, 5mM MgCl2 90% H2O/10% D2O 55 6.5 288 5 2D 1H-13C HSQC 2.0 mM [U-100% 13C; U-100% 15N] J345-2-2, 5mM MgCl2 100% D2O 55 6.5 298 6 3D 13C-edited HMQC-NOESY 2.0 mM [U-100% 13C; U-100% 15N] J345-2-2, 5mM MgCl2 100% D2O 55 6.5 298 7 3D CT-HCCH-COSY 2.0 mM [U-100% 13C; U-100% 15N] J345-2-2, 5mM MgCl2 100% D2O 55 6.5 298 8 3D HCCH-TOCSY 2.0 mM [U-100% 13C; U-100% 15N] J345-2-2, 5mM MgCl2 100% D2O 55 6.5 298 9 3D 15N-edited NOESY-HSQC 2.0 mM [U-100% 13C; U-100% 15N] J345-3-3, 5mM MgCl2 90% H2O/10% D2O 55 6.5 298 10 2D H(NC)-TOCSY-(C)H for guanosine residues 2.0 mM [U-100% 13C; U-100% 15N] J345-3-3, 5mM MgCl2 90% H2O/10% D2O 55 6.5 298 11 2D 1H-13C HMQC 2.0 mM [U-100% 13C; U-100% 15N] J345-2-2, 5mM MgCl2 100% D2O 55 6.5 298 12 2D 1H-15N MQ-(HC)N(C)H 2.0 mM [U-100% 13C; U-100% 15N] J345-2-2, 5mM MgCl2 100% D2O 55 6.5 298 13 2D 1H-15N CPMG-NOESY 1.5-2.0 mM [U-100% 15N] J345-1-1, 5mM MgCl2 90% H2O/10% D2O 55 6.5 288 14 2D HNN-COSY 1.5-2.0 mM [U-100% 15N] J345-1-1, 5mM MgCl2 90% H2O/10% D2O 55 6.5 288
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian UNITY 600
NMR Refinement Method Details Software simulated annealing NMRDraw
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 200 Conformers Submitted Total Number 21 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 data analysis NMRDraw Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 2 processing NMRDraw Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 3 data analysis NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 4 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 5 chemical shift assignment CCPNMR_suite CCPN 6 data analysis CCPNMR_suite CCPN 7 peak picking CCPNMR_suite CCPN 8 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 9 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 10 structure analysis PyMOL Schrodinger 11 structure display PyMOL Schrodinger