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.
