☰ Navigation Tabs
Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') 95% H2O/5% D2O 0.1 M 6.2 ambient 273 Varian INOVA 600 2 2D 1H-1H TOCSY 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') 95% H2O/5% D2O 0.1 M 6.2 ambient 273 Varian INOVA 600 3 2D 1H-1H NOESY 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') 100% D2O 0.1 M 6.2 ambient 283 Varian INOVA 600 4 2D 1H-1H TOCSY 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') 100% D2O 0.1 M 6.2 ambient 283 Varian INOVA 600 5 2D 31P-1H COSY 3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') 100% D2O 0.1 M 6.2 ambient 283 Varian INOVA 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian INOVA 600
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest restraint energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 33 Representative Model 1 (lowest restraint energy)
Computation: NMR Software # Classification Version Software Name Author 1 collection VNMR 6.1C Varian 2 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 3 processing NMRDraw Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 4 chemical shift assignment Sparky Goddard 5 data analysis Sparky Goddard 6 refinement Amber 14 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 7 data analysis Amber 14 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 8 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman