2RP1
Refined solution structure of the PEMV-1 mRNA pseudoknot, regularized average structure
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D 1H-13C NOESY | 2 mM [U-100% 13C; U-100% 15N] RNA, 10 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM DSS, 5 mM magnesium chloride | 100% D2O | 6 | ambient | 298 | ||
2 | 2D 1H-1H NOESY | 2 mM RNA, 10 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM DSS, 5 mM magnesium chloride | 90% H2O/10% D2O | 6 | ambient | 298 | ||
3 | J-modulated CT-HSQC | 2 mM [U-100% 13C; U-100% 15N] RNA, 10 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM DSS, 20 mg/ml Pf1 phage, 5 mM magnesium chloride | 100% D2O | 6 | ambient | 298 | ||
4 | CT-TROSY | 2 mM [U-100% 13C; U-100% 15N] RNA, 10 mM potassium phosphate, 100 mM potassium chloride, 0.1 mM DSS, 20 mg/ml Pf1 phage, 5 mM magnesium chloride | 100% D2O | 6 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 900 |
2 | Bruker | AVANCE | 800 |
3 | Varian | INOVA | 500 |
4 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | X-PLOR NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 28 |
Conformers Submitted Total Number | 1 |
Representative Model | (minimized average structure) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra, Clore | |
2 | chemical shift assignment | Sparky | Goddard | |
3 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | peak picking | Felix | Accelrys Software Inc. |