7SHX
A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript, NMR, minimized average structure
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-13C HSQC | 1.0 mM [U-100% 13C; U-100% 15N] paRNA | 95% H2O/5% D2O | 20 mM | 6.0 | 1 atm | 298 | Bruker AVANCE III 800 |
2 | 2D 1H-15N HSQC | 1.0 mM [U-100% 13C; U-100% 15N] paRNA | 95% H2O/5% D2O | 20 mM | 6.0 | 1 atm | 298 | Bruker AVANCE III 800 |
3 | 2D 1H-1H NOESY | 1.0 mM [U-100% 13C; U-100% 15N] paRNA | 95% H2O/5% D2O | 20 mM | 6.0 | 1 atm | 298 | Bruker AVANCE III 800 |
5 | 2D 1H-1H TOCSY | 1.0 mM [U-100% 13C; U-100% 15N] paRNA | 95% H2O/5% D2O | 20 mM | 6.0 | 1 atm | 298 | Bruker AVANCE III 600 |
6 | 1D 1H | 1.0 mM [U-100% 13C; U-100% 15N] paRNA | 95% H2O/5% D2O | 20 mM | 6.0 | 1 atm | 298 | Bruker AVANCE III 600 |
7 | 3D 1H-13C NOESY aliphatic | 1.0 mM [U-100% 13C; U-100% 15N] paRNA | 95% H2O/5% D2O | 20 mM | 6.0 | 1 atm | 298 | Bruker AVANCE III 800 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 800 |
2 | Bruker | AVANCE III | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | X-PLOR NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (minimized average structure) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
2 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard |