2K65
NMR solution structure of the exon/intron binding site 1 (EBS1/IBS1) of the group II intron Sc.ai5(gamma)
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA | 100% D2O | 100 | 6.3 | ambient | 288 | |
2 | 2D 1H-1H NOESY | 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA | 100% D2O | 100 | 6.3 | ambient | 293 | |
3 | 2D 1H-1H NOESY | 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA | 100% D2O | 100 | 6.3 | ambient | 298 | |
4 | 2D 1H-1H TOCSY | 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA | 100% D2O | 100 | 6.3 | ambient | 288 | |
5 | 2D 1H-1H TOCSY | 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA | 100% D2O | 100 | 6.3 | ambient | 293 | |
6 | 2D 1H-1H TOCSY | 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA | 100% D2O | 100 | 6.3 | ambient | 298 | |
7 | 2D 1H-1H NOESY | 0.9 mM RNA (7A-MER), 0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA | 90% H2O/10% D2O | 100 | 6.3 | ambient | 278 | |
8 | 2D 1H-13C HSQC | 0.8-0.9 mM RNA (7A-MER), 0.8-0.9 mM RNA (7B-MER), 100 mM potassium chloride, 10 uM EDTA | 100% D2O | 100 | 6.3 | ambient | 288 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 700 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle dynamics, simulated annealing | TopSpin |
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 | processing | TopSpin | 1.3, 2.0, 2.1 | Bruker Biospin |
2 | chemical shift assignment | Sparky | 3.1 | Goddard |
3 | data analysis | Sparky | 3.1 | Goddard |
4 | peak picking | Sparky | 3.1 | Goddard |
5 | structure solution | DYANA | 1.5 | Guntert, Braun and Wuthrich |
6 | structure solution | CNSSOLVE | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
7 | refinement | X-PLOR NIH | 2.16 | Schwieters, Kuszewski, Tjandra and Clore |