2KD4
Solution structure and thermodynamics of 2',5' RNA intercalation
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 1H-1H NOESY | 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4 | 99.9% D2O | 260 | 6.5 | 1 atm | 282 | |
2 | 31P-1H HETCOR | 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4 | 99.9% D2O | 260 | 6.5 | 1 atm | 282 | |
3 | 1H-1H TOCSY | 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4 | 99.9% D2O | 260 | 6.5 | 1 atm | 282 | |
4 | 31P-decoupled 1H-1H COSY | 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4 | 99.9% D2O | 260 | 6.5 | 1 atm | 282 | |
5 | 1H-1H NOESY with WATERGATE water suppression | 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4 | 99.9% D2O | 130 | 1 atm | 282 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
2 | Bruker | DRX | 500 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | 300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealed | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | Bruker Biospin | |
2 | data analysis | XwinNMR | Bruker Biospin | |
3 | processing | XwinNMR | Bruker Biospin | |
4 | chemical shift assignment | Sparky | Goddard | |
5 | data analysis | Sparky | Goddard | |
6 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm | |
7 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm |