tRNAPhe-based homology model for tRNAVal refined against base N-H RDCs in two media and SAXS data
SOLUTION NMR - SOLUTION SCATTERING
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N TROSY-HSQC | 0.5 mM [U-100% 15N] RNA (76-MER), 10 mM sodium phosphate, 80 mM sodium chloride, 5 mM magnesium chloride, 0.1 mM EDTA | 90% H2O/10% D2O | 0.155 | 6.8 | ambient atm | 298 | |
| 2 | 2D 1H-15N HSQC | 0.5 mM [U-100% 15N] RNA (76-MER), 10 mM sodium phosphate, 80 mM sodium chloride, 5 mM magnesium chloride, 0.1 mM EDTA | 90% H2O/10% D2O | 0.155 | 6.8 | ambient atm | 298 | |
| 3 | 2D 1H-15N TROSY-HSQC | 0.5 mM [U-100% 15N] RNA (76-MER), 10 mM sodium phosphate, 80 mM sodium chloride, 5 mM magnesium chloride, 0.1 mM EDTA | 90% H2O/10% D2O | 0.155 | 6.8 | ambient atm | 298 | |
| 4 | 2D 1H-15N HSQC | 0.5 mM [U-100% 15N] RNA (76-MER), 10 mM sodium phosphate, 80 mM sodium chloride, 5 mM magnesium chloride, 0.1 mM EDTA | 90% H2O/10% D2O | 0.155 | 6.8 | ambient atm | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 800 |
| 2 | Bruker | DMX | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing/torsion angle dynamics | tRNAVal solution structure is obtained by refinement of the tRNAPhe based homology model against RDC data (base N-H RDCs) from Pf1 and self-alignment (MSA), and SAXS data. Totals of 24 Pf1 RDCs and 20 MSA RDcs were fitted. During the refinement, the local geometry was kept close to the tRNAPhe based homology model using a set of non-crystallographic symmetry restraint terms. The NCS potentials included: 70 sequential i/i+1 terms and 34 additional terms for base pairs and triplets. The experimental SAXS data between q=0.03 and 0.35 A^-1 were fitted as well. | X-PLOR NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 3 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR NIH | 2.9.14 | Schwieters, Kuszewski, Tjandra and Clore |
| 2 | refinement | CNS | 1.0 | Brunger, Adams, Clore, Gros, Nilges and Read |
