Table 4.
Rotational diffusion tensor characteristics for D5 derived using ROTDIF from A and G base CH 13C relaxation data for axially-symmetric diffusion tensor model.
| Method | Nucleotides | Dx * | Dy | Dz | α* | β | γ | τc * | ζ | η |
|---|---|---|---|---|---|---|---|---|---|---|
| Published (Eldho and Dayie, 2007) | -SLa, -IBb, -CTc | 2.5 ±0.1 | 2.5 ±0.1 | 3.4 ±0.2 | 69 ±7 | 98 ±15 | - - |
6.0 ±0.3 | 1.4 ±0.2 | - - |
| ROTDIF 3 | -SL, -IB, -CT | 1.81 ±0.05 | 3.11 ±0.04 | 3.11 ±0.04 | 126 ±42 | 3 ±2 | - - |
6.23 ±0.04 | 0.58 ±0.02 | - - |
| ROTDIF 3 | -SL, -IB | 1.78 ±0.04 | 3.12 ±0.05 | 3.12 ±0.05 | 128 ±24 | 5 ±2 | - - |
6.23 ±0.05 | 0.57 ±0.02 | - - |
| ROTDIF 3 | -SL, -CT | 1.99 ±0.02 | 2.84 ±0.02 | 2.84 ±0.02 | 103 ±2 | 18 ±2 | - - |
6.51 ±0.03 | 0.70 ±0.01 | - - |
| ROTDIF 3 | -IB, -CT | 2.01 ±0.02 | 2.93 ±0.03 | 2.93 ±0.03 | 101 ±43 | 2 ±1 | - - |
6.35 ±0.03 | 0.68 ±0.01 | - - |
| ROTDIF 3 | -SL | 2.01 ±0.02 | 2.83 ±0.02 | 2.83 ±0.02 | 108 ±2 | 19 ±2 | - - |
6.52 ±0.02 | 0.71 ±0.01 | - - |
| ROTDIF 3 | -IB | 1.99 ±0.03 | 2.92 ±0.03 | 2.92 ±0.03 | 105 ±2 | 6 ±2 | - - |
6.38 ±0.03 | 0.68 ±0.02 | - - |
| ROTDIF 3 | -CT | 2.02 ±0.02 | 2.86 ±0.02 | 2.86 ±0.02 | 95 ±2 | 12 ±2 | - - |
6.46 ±0.02 | 0.70 ±0.01 | - - |
| ROTDIF 3 (Robust) | all | 2.02 ±0.44 | 2.84 ±0.75 | 2.84 ±0.75 | 96 ±117 | 16 ±47 | - - |
6.50 ±0.25 | 0.71 ±0.91 | - - |
| ELM | - | 1.57 | 2.33 | 4.53 | 135 | 77 | 109 | 5.94 | 2.32 | 0.44 |
a
Without Stem Loop
b
Without Internal Bulge
c
Without Catalytic Triad
*
The units are 107s−1 for Dx, Dy, Dz, ns for τc, and degrees for α, β, and γ angles.