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NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
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 90% H2O/10% D2O 55 6.5 288 2 2D 1H-15N HSQC 1.5-2.0 mM [U-100% 15N] J345 90% H2O/10% D2O 55 6.5 288 3 2D 1H-15N HSQC NH2 only 1.5-2.0 mM [U-100% 15N] J345 90% H2O/10% D2O 55 6.5 288 4 3D 1H-15N NOESY 1.5-2.0 mM [U-100% 15N] J345 90% H2O/10% D2O 55 6.5 288 5 2D 1H-13C HSQC 2.0 mM [U-100% 13C; U-100% 15N] J345 100% D2O 55 6.5 298 6 3D 13C-edited HMQC-NOESY 2.0 mM [U-100% 13C; U-100% 15N] J345 100% D2O 55 6.5 298 7 3D CT-HCCH-COSY 2.0 mM [U-100% 13C; U-100% 15N] J345 100% D2O 55 6.5 298 8 3D HCCH-TOCSY 2.0 mM [U-100% 13C; U-100% 15N] J345 100% D2O 55 6.5 298 9 3D 15N-edited NOESY-HSQC 2.0 mM [U-100% 13C; U-100% 15N] J345 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 90% H2O/10% D2O 55 6.5 298 11 2D 1H-13C HMQC 2.0 mM [U-100% 13C; U-100% 15N] J345 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 100% D2O 55 6.5 298 13 2D 1H-15N CPMG-NOESY 1.5-2.0 mM [U-100% 15N] J345 90% H2O/10% D2O 55 6.5 288 14 2D HNN-COSY 1.5-2.0 mM [U-100% 15N] J345 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 300 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