2P89
Solution structure of the 3' pseudouridyation pocket of U65 snoRNA with bound substrate
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 5 mM Sodium phosphate buffer, pH 6.0 | 90% H2O/10% D2O | 5 mM | 6 | ambient | 288 | |
2 | 2D NOESY | 5 mM Sodium phosphate buffer, pH 6.0 | D2O | 5 mM | 6 | ambient | 288 | |
3 | 13C-Filter/edited 2D NOESY | 5 mM Sodium phosphate buffer, pH 6.0 | D2O | 5 mM | 6 | ambient | 288 | |
4 | 3D_13C-separated_NOESY | 5 mM Sodium phosphate buffer, pH 6.0 | D2O | 5 mM | 6 | ambient | 288 | |
5 | HSQC | 5 mM Sodium phosphate buffer, pH 6.0 | D2O | 5 mM | 6 | ambient | 288 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Bruker | DRX | 600 |
3 | Bruker | DRX | 800 |
NMR Refinement | ||
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Method | Details | Software |
distance geometry simulated annealing | the structures are based on 768 NOE-derived distance constraints, 404 dihedral angle restraints,106 distance restraints from hydrogen bonds, 32 RDC restraints | XwinNMR |
NMR Ensemble Information | |
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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 | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 3.1 | Bruker |
2 | processing | XwinNMR | 3.1 | Bruker |
3 | data analysis | Sparky | 3.113 | T.D. Goddard and D. G. Kneller |
4 | refinement | X-PLOR | NIH | Brunger |