2K96
Solution structure of the RDC-refined P2B-P3 pseudoknot from human telomerase RNA (delta U177)
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D JNN-HNN COSY | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O | 95% H2O/5% D2O | 6.3 | ambient | 283 | ||
2 | 2D 1H-15N HSQC | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O | 95% H2O/5% D2O | 6.3 | ambient | 283 | ||
3 | 2D 1H-13C S3CT HSQC | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 100 % D2O | 100% D2O | 6.3 | ambient | 293 | ||
4 | 2D 15N CPMG NOESY | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O | 95% H2O/5% D2O | 6.3 | ambient | 283 | ||
5 | 2D 1H-1H NOESY | 1 mM [U-98% 13C; U-98% 15N] PKDU, 10 mM sodium phosphate, 200 mM potassium chloride, 50 uM EDTA, 95 % H2O, 5 % D2O | 95% H2O/5% D2O | 6.3 | ambient | 283 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Bruker | DRX | 600 |
3 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | PDB entry 2k96 is a better refined structure of entry 1ymo with additional RDCs | X-PLOR NIH |
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 | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | X-PLOR NIH | 2.9.8 | Schwieters, Kuszewski, Tjandra and Clore |
2 | refinement | X-PLOR NIH | 2.9.8 | Schwieters, Kuszewski, Tjandra and Clore |
3 | data analysis | MOLMOL | 2k.2 | Koradi, Billeter and Wuthrich |
4 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
5 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
6 | data analysis | NMRView | Johnson, One Moon Scientific | |
7 | chemical shift assignment | Sparky | Goddard | |
8 | data analysis | Sparky | Goddard | |
9 | collection | XwinNMR | Bruker Biospin | |
10 | processing | XwinNMR | Bruker Biospin |