2N7X
Solution structure of microRNA 20b pre-element
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 1 mM miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride | 90% H2O/10% D2O | 6.5 | ambient atm | 279 | ||
2 | 2D 1H-1H NOESY | 1 mM miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride | 100% D2O | 6.5 | ambient atm | 298 | ||
3 | 2D 1H-1H TOCSY | 1 mM miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride | 100% D2O | 6.5 | ambient atm | 298 | ||
4 | 2D 1H-13C HSQC | 1 mM [U-99% 13C; U-99% 15N] miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride | 100% D2O | 6.5 | ambient atm | 298 | ||
5 | 3D 1H-13C NOESY | 1 mM [U-99% 13C; U-99% 15N] miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride | 100% D2O | 6.5 | ambient atm | 298 | ||
6 | 2D 1H-15N HSQC | 1 mM [U-99% 13C; U-99% 15N] miR-20b, 10 mM sodium phosphate, 20 mM sodium chloride | 90% H2O/10% D2O | 6.5 | ambient atm | 279 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 800 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
restrained simulated annealing | TopSpin |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | Bruker Biospin | |
2 | structure solution | CYANA | Guntert, Mumenthaler and Wuthrich | |
3 | chemical shift assignment | CcpNMR | CCPN | |
4 | peak picking | CcpNMR | CCPN | |
5 | data analysis | CcpNMR | CCPN | |
6 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
7 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
8 | geometry optimization | TALOS | Cornilescu, Delaglio and Bax |