2GBH
NMR structure of stem region of helix-35 of 23S E.coli ribosomal RNA (residues 736-760)
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | RDC measurement | 1.5mM helix-35psi U-15N,13C; 17mM NaCl, 17mM phosphate buffer; 99% D2O | 99% D2O | 17 mM NaCl, 17 mM phosphate | 6.8 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 800 |
| 2 | Bruker | DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Cartesian simulated annealing | Experimental restraints for the helix-35 stem are 277 RDCs, 13 31P anisotropic shifts, 41 dihedral angles and 188 NOEs. During the refinement the geometries of selected ribose rings were kept identical with the NCS restraint terms. Attractive non-bonded potentials were employed. No database-derived terms were used. The parameter file was modified with nucleotide type-specific values for distances, angles and improper torsions. Cross-validation statistics on the groups of 1/4 of ribose 1-bond C-H RDCs corresponds to an average Q-factor of 0.135. | Xplor-NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 5 |
| Conformers Submitted Total Number | 5 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | Xplor-NIH | 2.9.4 | Schwieters, Kuszewski, Tjandra, Clore |
