2L5D
Solution Structures of human PIWI-like 1 PAZ domain with ssRNA (5'-pUGACA)
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D HNCACB | 100 mM sodium phosphate-4, 150 mM sodium chloride-5, 5 mM [U-100% 2H] DTT-6 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
2 | 3D HN(COCA)CB | 100 mM sodium phosphate-4, 150 mM sodium chloride-5, 5 mM [U-100% 2H] DTT-6 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
3 | 3D 1H-15N NOESY | 100 mM sodium phosphate-4, 150 mM sodium chloride-5, 5 mM [U-100% 2H] DTT-6 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
4 | 3D 1H-13C NOESY | 100 mM sodium phosphate-1, 150 mM sodium chloride-2, 5 mM [U-100% 2H] DTT-3 | 100% D2O | 6.5 | ambient | 298 | ||
5 | 3D 13C-Edited-13C/15N-filtered NOESY | 100 mM sodium phosphate-1, 150 mM sodium chloride-2, 5 mM [U-100% 2H] DTT-3 | 100% D2O | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 600 |
3 | Bruker | DRX | 500 |
4 | Bruker | AVANCE | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
DGSA-distance geometry simulated annealing, torsion angle dynamics | ARIA |
NMR Ensemble Information | |
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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 | refinement | ARIA | 2.2 | Linge, O'Donoghue and Nilges |
2 | processing | NMRPipe | 2.3 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
3 | chemical shift calculation | NMRPipe | 2.3 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
4 | peak picking | NMRView | 5.04 | Johnson, One Moon Scientific |
5 | chemical shift assignment | NMRView | 5.04 | Johnson, One Moon Scientific |
6 | data analysis | NMRView | 5.04 | Johnson, One Moon Scientific |
7 | structure solution | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |