2LBS
Solution structure of double-stranded RNA binding domain of S. cerevisiae RNase III (Rnt1p) in complex with AAGU tetraloop hairpin
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
2 | 2D 1H-1H TOCSY | 0.8-1 mM protein, 1-2 mM [U-100% 13C; U-100% 15N] DNA/RNA hybrid | 100% D2O | 0.15 | 6.5 | ambient | 298 | |
3 | 2D 1H-1H NOESY | 0.8-1 mM protein, 1-2 mM [U-100% 13C; U-100% 15N] DNA/RNA hybrid | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
4 | 3D CBCA(CO)NH | 0.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
5 | 3D HNCACB | 0.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
6 | 3D HCCH-TOCSY | 0.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid | 100% D2O | 0.15 | 6.5 | ambient | 298 | |
7 | 3D HCCH-COSY | 0.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid | 100% D2O | 0.15 | 6.5 | ambient | 298 | |
8 | 3D 1H-15N NOESY | 0.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 | |
9 | 3D 1H-13C NOESY | 0.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid | 100% D2O | 0.15 | 6.5 | ambient | 298 | |
10 | 2D 1H-1H COSY | 0.8-1 mM protein, 1-2 mM [U-100% 13C; U-100% 15N] DNA/RNA hybrid | 100% D2O | 0.15 | 6.5 | ambient | 298 | |
11 | 2D FILTERED/EDITED NOESY | 0.8-1 mM protein, 1-2 mM [U-100% 13C; U-100% 15N] DNA/RNA hybrid | 100% D2O | 0.15 | 6.5 | ambient | 298 | |
12 | 2D 1H-15N HSQC IPAP | 0.8-1 mM [U-100% 13C; U-100% 15N] protein, 1-2 mM DNA/RNA hybrid | 90% H2O/10% D2O | 0.15 | 6.5 | ambient | 298 |
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 |
torsion angle dynamics | X-PLOR NIH |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 16 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | X-PLOR NIH | 2.24 | Schwieters, Kuszewski, Tjandra and Clore |
2 | refinement | X-PLOR NIH | 2.24 | Schwieters, Kuszewski, Tjandra and Clore |
3 | chemical shift assignment | NMRView | 5.2.2 | Johnson, One Moon Scientific |
4 | data analysis | NMRView | 5.2.2 | Johnson, One Moon Scientific |
5 | peak picking | NMRView | 5.2.2 | Johnson, One Moon Scientific |
6 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
7 | data analysis | TALOS | Cornilescu, Delaglio and Bax | |
8 | collection | TopSpin | 2.0 | Bruker Biospin |
9 | collection | XwinNMR | Bruker Biospin | |
10 | data analysis | ProcheckNMR | Laskowski and MacArthur |