2K66
NMR solution structure of the d3'-stem closed by a GAAA tetraloop of the group II intron Sc.ai5(gamma)
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 100% D2O | 10 | 6.0-6.1 | ambient | 293 | |
2 | 2D 1H-1H NOESY | 0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 100% D2O | 10 | 6.0-6.1 | ambient | 303 | |
3 | 2D 1H-1H TOCSY | 0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 100% D2O | 10 | 6.0-6.1 | ambient | 293 | |
4 | 2D 1H-1H TOCSY | 0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 100% D2O | 10 | 6.0-6.1 | ambient | 303 | |
5 | 2D 1H-1H NOESY | 0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 90% H2O/10% D2O | 10 | 6.2 | ambient | 278 | |
6 | 2D 1H-1H NOESY | 0.9-1.3 mM RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 90% H2O/10% D2O | 10 | 6.2 | ambient | 293 | |
7 | 2D 1H-13C HSQC | 1.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 100% D2O | 10 | 6.4 | ambient | 303 | |
8 | 2D 1H-15N HSQC | 1.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 90% H2O/10% D2O | 10 | 6.4 | ambient | 278 | |
9 | 2D JNN HNN-COSY | 1.0 mM [U-100% 13C; U-100% 15N] RNA (22-MER), 10 mM potassium chloride, 10 uM EDTA | 90% H2O/10% D2O |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | Avance | 700 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
torsion angle dynamics, simulated annealing | TOPSPIN |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | processing | TOPSPIN | 1.3, 2.0, 2.1 | Bruker Biospin |
2 | chemical shift assignment | SPARKY | 3.1 | Goddard |
3 | data analysis | SPARKY | 3.1 | Goddard |
4 | peak picking | SPARKY | 3.1 | Goddard |
5 | structure solution | DYANA | 1.5 | Guntert, Braun and Wuthrich |
6 | structure solution | CNSSOLVE | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
7 | refinement | X-PLOR_NIH | 2.16 | Schwieters, Kuszewski, Tjandra and Clore |