RDC refined solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (rnt1p) in complex with the terminal RNA hairpin of snr47 precursor
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
| 2 | 3D HNCACB | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
| 3 | 3D HBHA(CO)NH | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
| 4 | 3D HNCO | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
| 5 | 3D HCCH-TOCSY | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % [U-100% 2H] D2O, 10 % sodium chloride, 150 mM sodium phosphate | 100% D2O | 150 | 6.5 | ambient | 298 | |
| 6 | 3D HCCH-COSY | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % [U-100% 2H] D2O, 10 % sodium chloride, 150 mM sodium phosphate | 100% D2O | 150 | 6.5 | ambient | 298 | |
| 7 | 3D 1H-15N NOESY | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % H2O, 10 % [U-100% 2H] D2O, 20 mM sodium phosphate, 150 mM sodium chloride | 90% H2O/10% D2O | 150 | 6.5 | ambient | 298 | |
| 8 | 3D 1H-13C NOESY | 1 mM [U-100% 13C; U-100% 15N] protein, 90 % [U-100% 2H] D2O, 10 % sodium chloride, 150 mM sodium phosphate | 100% D2O | 150 | 6.5 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| 2 | Bruker | DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | THIS STRUCTURE IS AN RDC REFINED STRUCTURE OF PDB ENTRY 1T4L USING THE SAME RESTRAINTS PLUS ADDITIONAL RDCS [81 RDCS (REFINED) VS 43 RDCS (1T4L)]. | TopSpin |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 16 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | Bruker Biospin | |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 4 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
| 5 | data analysis | TALOS | Cornilescu, Delaglio and Bax | |
| 6 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 7 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
