Solution structure of the RDC-refined P2B-P3 pseudoknot from human telomerase RNA (delta U177)
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D JNN-HNN COSY | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O | 95% H2O/5% D2O | 6.3 | ambient | 283 | ||
| 2 | 2D 1H-15N HSQC | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O | 95% H2O/5% D2O | 6.3 | ambient | 283 | ||
| 3 | 2D 1H-13C S3CT HSQC | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 100 % D2O | 100% D2O | 6.3 | ambient | 293 | ||
| 4 | 2D 15N CPMG NOESY | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O | 95% H2O/5% D2O | 6.3 | ambient | 283 | ||
| 5 | 2D 1H-1H NOESY | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O | 95% H2O/5% D2O | 6.3 | ambient | 283 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| 2 | Bruker | DRX | 600 |
| 3 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | PDB entry 2k96 is a better refined structure of entry 1ymo with additional RDCs | X-PLOR NIH |
| 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 | structure solution | X-PLOR NIH | 2.9.8 | Schwieters, Kuszewski, Tjandra and Clore |
| 2 | refinement | X-PLOR NIH | 2.9.8 | Schwieters, Kuszewski, Tjandra and Clore |
| 3 | data analysis | MOLMOL | 2k.2 | Koradi, Billeter and Wuthrich |
| 4 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 5 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 6 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 7 | chemical shift assignment | Sparky | Goddard | |
| 8 | data analysis | Sparky | Goddard | |
| 9 | collection | XwinNMR | Bruker Biospin | |
| 10 | processing | XwinNMR | Bruker Biospin | |
