1R2P
Solution structure of domain 5 from the ai5(gamma) group II intron
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 0.5 - 0.7 mM D5 RNA; 0 - 200mM KCl, 0 - 20 mM MgCl2, 0.01 mM EDTA, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100mM KCl | 6.5 | 278 | ||
2 | 2D NOESY | 0.5 - 0.7 mM D5 RNA; 0 - 200mM KCl, 0 - 20 mM MgCl2, 0.01 mM EDTA | 99.999% D2O | 100mM KCl | 6.5 | 308 | ||
3 | 2D NOESY | 0.5 - 0.7 mM D5 RNA; 0 - 200mM KCl, 0 - 20 mM MgCl2, 0.01 mM EDTA | 99.999% D2O | 100mM KCl | 6.5 | 291 | ||
4 | 3D_13C-separated_NOESY | 0.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA | 99.999% D2O | 100mM KCl | 6.5 | 298 | ||
5 | 2D 1H-13C HSQC | 0.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA | 99.999% D2O | 100mM KCl | 6.5 | 298 | ||
6 | 2D 1H-1H TOCSY | 0.5 - 0.7 mM D5 RNA; 0 - 200mM KCl, 0 - 20 mM MgCl2, 0.01 mM EDTA | 99.999% D2O | 100mM KCl | 6.5 | 298 | ||
7 | 3D 1H-13C-1H HCCH TOCSY | 0.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA | 99.999% D2O | 100mM KCl | 6.5 | 298 | ||
8 | 3D 1H-13C-1H HCCH COSY | 0.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA | 99.999% D2O | 100mM KCl | 6.5 | 298 | ||
9 | 2D 2JHN HNN-COSY | 0.5 - 0.7 mM D5 RNA, 13C-15N LABELED; 100mM KCl, 0.01 mM EDTA, 90% H2O, 10% D2O | 90% H2O/10% D2O | 100mM KCl | 6.5 | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | DMX | 500 |
3 | Bruker | DMX | 750 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
TORSION ANGLE MOLECULAR DYNAMICS CARTESIAN SPACE SIMULATED ANNEALING AND MOLECULAR DYNAMICS RESIDUAL DIPOLAR COUPLINGS | STRUCTURES BASED ON 678 NOE-DERIVED DISTANCE RESTRAINTS, 261 DIHEDRAL RESTRAINTS, 72 HYDROGEN BOND RESTRAINTS, AND 24 RESIDUAL DIPOLAR COUPLING RESTRAINTS | CNS |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
---|---|
Details | RESIDUAL DIPOLAR COUPLINGS WERE MEASURED USING 1H-13C HSQC COUPLED IN EITHER THE PROTON OR THE CARBON DIMENSION |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | structure solution | CNS | 1.1 | Brunger et. al. |
2 | data analysis | DYANA | Guntert, Mumenthaler, Wuthrich | |
3 | data analysis | Sparky | 3 | Goddard and Kneller |
4 | processing | XwinNMR | 2.6 | Bruker |
5 | refinement | CNS | 1.1 | Brunger et. al. |