Table 3. Average Structural Parameters for the DDD System Obtained by Averaging Values Calculated from the Trajectory Snapshots from the 1 ms Aggregated Trajectories for Each Combination of Force Field and Water Modela.
| exptl |
TIP3P |
OPC |
||||||
|---|---|---|---|---|---|---|---|---|
| NMR | X-ray | bsc0 | OL15 | bsc1 | bsc0 | OL15 | bsc1 | |
| shear/Å | 0.0 | 0.0 | 0.0 ± 0.11 | 0.0 ± 0.10 | 0.0 ± 0.11 | 0.0 ± 0.11 | 0.0 ± 0.10 | 0.0 ± 0.10 |
| stretch/Å | –0.34 | –0.23 | –0.2 ± 0.04 | –0.02 ± 0.04 | –0.02 ± 0.04 | –0.02 ± 0.04 | –0.03 ± 0.04 | –0.02 ± 0.04 |
| stagger/Å | –0.12 | 0.10 | 0.06 ± 0.16 | 0.0 ± 0.16 | 0.05 ± 0.16 | 0.07 ± 0.16 | 0.02 ± 0.15 | 0.06 ± 0.15 |
| buckle/deg | 0.02 | 0.2 | –0.02 ± 4.92 | 0.03 ± 4.64 | 0.01 ± 4.52 | –0.04 ± 4.59 | 0.04 ± 4.37 | 0.01 ± 4.32 |
| propeller/deg | –17.58 | –13.3 | –12.7 ± 3.09 | –12.26 ± 2.72 | –10.38 ± 2.89 | –12.59 ± 2.85 | –11.87 ± 2.62 | –9.91 ± 2.76 |
| opening/deg | –1.10 | 1.31 | 0.3 ± 1.19 | 0.1 ± 1.76 | –0.41 ± 1.70 | 0.18 ± 1.73 | 0.08 ± 1.66 | –0.46 ± 1.64 |
| shift/Å | 0.0 | 0.0 | 0.0 ± 0.19 | 0.0 ± 0.19 | 0.0 ± 0.20 | 0.0 ± 0.17 | 0.0 ± 0.18 | 0.0 ± 0.19 |
| tilt/deg | 0.01 | 0.3 | 0.0 ± 1.26 | 0.0 ± 1.23 | 0.01 ± 1.26 | 0.0 ± 1.21 | 0.01 ± 1.20 | 0.01 ± 1.22 |
| slide/Å | –0.21 | 0.07 | –0.4 ± 0.28 | 0.0 ± 0.26 | –0.27 ± 0.25 | –0.46 ± 0.26 | –0.12 ± 0.25 | –0.33 ± 0.24 |
| rise/Å | 3.2 | 3.3 | 3.31 ± 0.07 | 3.32 ± 0.06 | 3.31 ± 0.07 | 3.30 ± 0.07 | 3.31 ± 0.06 | 3.30 ± 0.6 |
| roll/deg | 3.03 | 1.98 | 3.5 ± 2.13 | 2.8 ± 1.99 | 2.28 ± 1.89 | 2.91 ± 2.06 | 2.10 ± 1.98 | 2.10 ± 1.84 |
| twist/deg | 35.7 | 34.2 | 32.86 ± 1.59 | 35.21 ± 1.32 | 34.64 ± 1.43 | 33.37 ± 1.55 | 35.55 ± 1.34 | 34.73 ± 1.43 |
| X displacement/Å | –0.81 | –0.23 | –1.48 ± 0.66 | –0.56 ± 0.54 | –0.94 ± 0.57 | –1.46 ± 0.62 | –0.61 ± 0.53 | –1.01 ± 0.56 |
| Y displacement/Å | 0.0 | 0.1 | 0.0 ± 0.37 | 0.0 ± 0.28 | 0.0 ± 0.30 | 0.0 ± 0.32 | –0.01 ± 0.26 | 0.0 ± 0.29 |
| helical rise/Å | 3.18 | 3.29 | 3.18 ± 0.14 | 3.29 ± 0.10 | 3.26 ± 0.12 | 3.18 ± 0.13 | 3.27 ± 0.10 | 3.24 ± 0.11 |
| helical inclination/deg | 5.0 | 4.0 | 6.72 ± 4.11 | 4.88 ± 3.44 | 4.26 ± 3.40 | 5.79 ± 3.89 | 3.68 ± 3.42 | 3.97 ± 3.32 |
| tip/deg | 0.0 | –0.7 | 0.0 ± 2.48 | 0.0 ± 2.12 | –0.01 ± 2.22 | –0.01 ± 2.29 | –0.01 ± 2.05 | –0.02 ± 2.15 |
| helical twist/deg. | 36.0 | 34.6 | 34.07 ± 1.50 | 36.19 ± 1.27 | 35.61 ± 1.38 | 34.47 ± 1.44 | 36.43 ± 1.28 | 35.64 ± 1.38 |
| major width/Å | 19.56 | 19.12 | 19.88 ± 0.33 | 19.34 ± 0.26 | 19.51 ± 0.29 | 19.95 ± 0.28 | 19.41 ± 0.25 | 19.58 ± 0.26 |
| minor width/Å | 12.2 | 12.2 | 12.51 ± 0.20 | 12.26 ± 0.15 | 12.37 ± 0.17 | 12.54 ± 0.17 | 12.27 ± 0.14 | 12.37 ± 0.14 |
| pucker/deg | 137.1 | 129.5 | 130.5 ± 8.21 | 148.3 ± 6.02 | 149.7 ± 6.94 | 130.7 ± 7.78 | 148.5 ± 5.83 | 149.7 ± 6.43 |
| α/deg | 298.8 | 299.2 | 288.6 ± 4.60 | 289.5 ± 4.37 | 285.6 ± 6.03 | 289.3 ± 4.69 | 290.5 ± 4.32 | 286.1 ± 6.18 |
| β/deg | 172.4 | 175.7 | 168.1 ± 3.92 | 167.3 ± 5.16 | 164.4 ± 6.20 | 168.4 ± 4.02 | 169.6 ± 5.27 | 165.5 ± 6.07 |
| γ/deg | 50.28 | 56.52 | 57.3 ± 4.32 | 54.0 ± 3.58 | 60.1 ± 7.68 | 57.4 ± 4.53 | 53.8 ± 3.50 | 59.7 ± 7.58 |
| δ/deg | 126.7 | 122.8 | 121.0 ± 4.63 | 131.6 ± 3.47 | 134.6 ± 3.87 | 120.8 ± 4.50 | 131.4 ± 3.38 | 134.4 ± 3.70 |
| ε/deg | 188.5 | 190.4 | 197.7 ± 7.57 | 199.0 ± 7.56 | 201.3 ± 5.34 | 194.8 ± 7.23 | 194.8 ± 7.90 | 199.8 ± 5.49 |
| ζ/deg | 257.1 | 251.3 | 254.6 ± 9.18 | 244.6 ± 7.52 | 245.6 ± 6.64 | 256.6 ± 8.49 | 247.5 ± 7.59 | 245.9 ± 6.70 |
| χ/deg | 249.2 | 243.9 | 241.7 ± 5.09 | 251.3 ± 3.77 | 247.5 ± 3.86 | 241.0 ± 4.82 | 250.9 ± 3.66 | 247.4 ± 3.75 |
a
The two terminal base pairs on each side of the DDD were excluded for the average value calculation. The standard deviations are shown alongside the averages. NMR data are average values from the PDB 1NAJ structure, and the X-ray data were calculated from the PDB 1BNA structure.