8CF2
Solution structure of the RNA helix formed by the 5'-end of U1 snRNA and an A-1 bulged 5'-splice site in complex with SMN-CY
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H TOCSY | 1 mM unlableled RNA helix, 1.5 mM unlabeld SMN-CY, 10 mM deuterated MES, 50 mM unlabeld sodium chloride | 100% D2O | 50 mM | 5.5 | atm atm | 293 | Bruker AVIII 700 |
2 | 2D 1H-1H NOESY | 1 mM unlableled RNA helix, 1.5 mM unlabeld SMN-CY, 10 mM deuterated MES, 50 mM unlabeld sodium chloride | 100% D2O | 50 mM | 5.5 | atm atm | 293 | Bruker AVIII 900 |
3 | 2D 1H-13C HSQC | 1 mM unlableled RNA helix, 1.5 mM unlabeld SMN-CY, 10 mM deuterated MES, 50 mM unlabeld sodium chloride | 100% D2O | 50 mM | 5.5 | atm atm | 293 | Bruker AVIII 700 |
4 | 2D 1H-1H COSY | 1 mM unlableled RNA helix, 1.5 mM unlabeld SMN-CY, 10 mM deuterated MES, 50 mM unlabeld sodium chloride | 100% D2O | 50 mM | 5.5 | atm atm | 293 | Bruker AVIII 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVIII | 900 |
2 | Bruker | AVIII | 700 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | Amber | |
molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with acceptable covalent geometry |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 14 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | 22 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
2 | structure calculation | CYANA | 3.98 | Guntert, Mumenthaler and Wuthrich |
3 | chemical shift assignment | CARA | Keller and Wuthrich | |
4 | peak picking | CARA | Keller and Wuthrich | |
5 | data analysis | Amber | 22 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |