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Data selection and force field matrices
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Data selection
The data selection based on individual standard deviations,
with stepwise skipping of data using the following rules.
Data selection rules
- Improper base steps are skipped, i.e.
- base steps containing a nick,
- base steps containing base mismatches.
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Redundant base steps.
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Terminal base steps
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Base steps / coords deviating more than 3.0 standard deviation from the average.
Generic base step:
Base steps GC, CG, AT, and TA are counted twice in the symmetrized
and non-symmetrized data set.
Coordinate statistics for each base pair step
| Step | N | Shift, Å | Slide, Å | Rise, Å | Tilt, deg | Roll, deg | Twist, deg |
| | |  |  |  |  |  |  |
| CG | 22 | -0.25(1.10) | 0.61(0.53) | 3.34(0.33) | 0.40(3.80) | 3.40(6.50) | 35.10(6.00) |
| CA | 86 | -0.03(0.56) | 0.42(0.82) | 3.33(0.28) | -0.20(3.30) | 4.80(5.50) | 36.10(4.80) |
| TA | 62 | -0.02(0.56) | 0.29(0.87) | 3.36(0.29) | 0.00(2.50) | 1.20(6.90) | 37.90(6.30) |
| AG | 72 | 0.07(0.66) | -0.41(0.49) | 3.36(0.27) | -1.60(3.30) | 5.10(4.70) | 31.80(4.30) |
| GG | 78 | -0.03(0.65) | -0.53(0.77) | 3.46(0.29) | 0.30(3.60) | 4.30(4.80) | 32.20(4.80) |
| AA | 118 | 0.00(0.50) | -0.17(0.38) | 3.28(0.21) | -1.00(3.00) | -0.20(4.60) | 35.90(3.50) |
| GA | 68 | -0.29(0.47) | -0.06(0.59) | 3.30(0.23) | -1.70(3.40) | 2.20(4.30) | 36.00(4.70) |
| AT | 47 | 0.15(0.53) | -0.63(0.26) | 3.25(0.26) | 0.30(2.30) | 0.50(4.60) | 30.90(3.30) |
| AC | 91 | 0.15(0.57) | -0.62(0.40) | 3.32(0.22) | 0.10(3.40) | 0.90(4.50) | 32.00(3.50) |
| GC | 27 | 0.01(0.82) | -0.13(0.62) | 3.30(0.20) | 0.90(4.00) | 0.60(5.00) | 35.60(4.30) |
| XX | 590 | -0.01(0.65) | -0.12(0.76) | 3.33(0.26) | -0.20(3.30) | 1.80(5.70) | 34.60(5.40) |
N is the number of base pairs of each type available in the database.
The standard deviation of the coordinates are shown in parenthesis.
XX is the generic base step (applying above described selection rules).
Effective force field matrix for each base step
| CG | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 1.43 | -0.05 | -0.31 | -0.29 | -0.04 | 0.04 |
| Slide | -0.05 | 3.73 | 1.26 | 0.03 | 0.02 | 0.04 |
| Rise | -0.31 | 1.26 | 10.70 | 0.35 | 0.02 | -0.04 |
| Tilt | -0.29 | 0.03 | 0.35 | 0.15 | 0.03 | -0.01 |
| Roll | -0.04 | 0.02 | 0.02 | 0.03 | 0.03 | 0.01 |
| Twist | 0.04 | 0.04 | -0.04 | -0.01 | 0.01 | 0.03 |
| CA | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 3.81 | 0.38 | -0.53 | -0.20 | -0.02 | -0.09 |
| Slide | 0.38 | 2.32 | 1.86 | 0.07 | 0.02 | -0.21 |
| Rise | -0.53 | 1.86 | 15.04 | 0.33 | 0.01 | -0.25 |
| Tilt | -0.20 | 0.07 | 0.33 | 0.11 | 0.01 | -0.01 |
| Roll | -0.02 | 0.02 | 0.01 | 0.01 | 0.04 | 0.02 |
| Twist | -0.09 | -0.21 | -0.25 | -0.01 | 0.02 | 0.07 |
| TA | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 3.51 | -0.32 | -1.96 | -0.11 | 0.06 | 0.04 |
| Slide | -0.32 | 2.15 | 3.10 | 0.07 | -0.07 | -0.20 |
| Rise | -1.96 | 3.10 | 19.27 | -0.06 | -0.34 | -0.59 |
| Tilt | -0.11 | 0.07 | -0.06 | 0.17 | 0.00 | 0.01 |
| Roll | 0.06 | -0.07 | -0.34 | 0.00 | 0.04 | 0.03 |
| Twist | 0.04 | -0.20 | -0.59 | 0.01 | 0.03 | 0.06 |
| AG | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 2.99 | 0.65 | 2.31 | -0.23 | 0.02 | 0.04 |
| Slide | 0.65 | 4.57 | 2.18 | -0.03 | -0.11 | -0.06 |
| Rise | 2.31 | 2.18 | 23.17 | -0.72 | -0.26 | -0.65 |
| Tilt | -0.23 | -0.03 | -0.72 | 0.12 | 0.00 | 0.01 |
| Roll | 0.02 | -0.11 | -0.26 | 0.00 | 0.06 | 0.03 |
| Twist | 0.04 | -0.06 | -0.65 | 0.01 | 0.03 | 0.09 |
| GG | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 3.71 | -0.05 | -0.78 | -0.29 | 0.07 | 0.18 |
| Slide | -0.05 | 2.02 | 0.51 | 0.11 | 0.05 | -0.08 |
| Rise | -0.78 | 0.51 | 16.44 | -0.57 | 0.04 | -0.16 |
| Tilt | -0.29 | 0.11 | -0.57 | 0.13 | 0.00 | -0.02 |
| Roll | 0.07 | 0.05 | 0.04 | 0.00 | 0.05 | 0.01 |
| Twist | 0.18 | -0.08 | -0.16 | -0.02 | 0.01 | 0.06 |
| AA | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 6.05 | 2.05 | 5.88 | -0.33 | -0.01 | 0.15 |
| Slide | 2.05 | 8.08 | 1.57 | -0.06 | -0.14 | -0.14 |
| Rise | 5.88 | 1.57 | 31.12 | -0.79 | 0.22 | 0.14 |
| Tilt | -0.33 | -0.06 | -0.79 | 0.14 | 0.01 | 0.00 |
| Roll | -0.01 | -0.14 | 0.22 | 0.01 | 0.06 | 0.03 |
| Twist | 0.15 | -0.14 | 0.14 | 0.00 | 0.03 | 0.10 |
| GA | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 6.34 | 1.43 | -0.56 | -0.22 | 0.06 | 0.20 |
| Slide | 1.43 | 3.78 | -0.81 | 0.09 | -0.10 | -0.14 |
| Rise | -0.56 | -0.81 | 24.69 | -0.77 | -0.12 | -0.30 |
| Tilt | -0.22 | 0.09 | -0.77 | 0.12 | -0.01 | -0.01 |
| Roll | 0.06 | -0.10 | -0.12 | -0.01 | 0.09 | 0.05 |
| Twist | 0.20 | -0.14 | -0.30 | -0.01 | 0.05 | 0.09 |
| AT | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 3.71 | 0.62 | -0.20 | -0.13 | -0.01 | 0.03 |
| Slide | 0.62 | 15.44 | 0.99 | 0.23 | 0.16 | 0.05 |
| Rise | -0.20 | 0.99 | 17.97 | 0.12 | -0.26 | -0.55 |
| Tilt | -0.13 | 0.23 | 0.12 | 0.20 | 0.02 | 0.00 |
| Roll | -0.01 | 0.16 | -0.26 | 0.02 | 0.06 | 0.03 |
| Twist | 0.03 | 0.05 | -0.55 | 0.00 | 0.03 | 0.12 |
| AC | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 3.28 | 0.22 | -1.68 | -0.10 | -0.01 | 0.01 |
| Slide | 0.22 | 6.78 | 3.43 | 0.01 | 0.04 | -0.03 |
| Rise | -1.68 | 3.43 | 24.35 | 0.13 | 0.06 | -0.23 |
| Tilt | -0.10 | 0.01 | 0.13 | 0.09 | 0.01 | 0.00 |
| Roll | -0.01 | 0.04 | 0.06 | 0.01 | 0.06 | 0.03 |
| Twist | 0.01 | -0.03 | -0.23 | 0.00 | 0.03 | 0.10 |
| GC | Shift | Slide | Rise | Tilt | Roll | Twist |
| Shift | 2.78 | 0.59 | -6.96 | -0.36 | 0.00 | 0.12 |
| Slide | 0.59 | 5.01 | 3.45 | -0.04 | 0.32 | -0.19 |
| Rise | -6.96 | 3.45 | 58.89 | 1.83 | 0.78 | -0.64 |
| Tilt | -0.36 | -0.04 | 1.83 | 0.13 | 0.03 | 0.00 |
| Roll | 0.00 | 0.32 | 0.78 | 0.03 | 0.09 | 0.03 |
| Twist | 0.12 | -0.19 | -0.64 | 0.00 | 0.03 | 0.10 |