The base morphology parameters were calculated using the program by M. Babcock (Babcock, M.S. and Olson, W.K., 1994, J. Mol. Biol., 237, 98-156). 3.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Checking Numbers and RMS Values CHAIN a BASE 1 G RMS = 0.347479E-01 CHAIN a BASE 2 G RMS = 0.348613E-01 CHAIN a BASE 3 A RMS = 0.143058E-01 CHAIN a BASE 4 G RMS = 0.350278E-01 CHAIN a BASE 5 G RMS = 0.347146E-01 CHAIN a BASE 6 A RMS = 0.142720E-01 CHAIN a BASE 7 G RMS = 0.347709E-01 CHAIN a BASE 8 A RMS = 0.142579E-01 CHAIN a BASE 9 A RMS = 0.141177E-01 CHAIN a BASE 10 G RMS = 0.347826E-01 CHAIN a BASE 11 A RMS = 0.141800E-01 CHAIN a BASE 12 A RMS = 0.142048E-01 CHAIN a BASE 13 T RMS = 0.778019E-02 CHAIN a BASE 14 T RMS = 0.791258E-02 CHAIN a BASE 15 C RMS = 0.204575E-01 CHAIN a BASE 16 T RMS = 0.781980E-02 CHAIN a BASE 17 T RMS = 0.803304E-02 CHAIN a BASE 18 C RMS = 0.202898E-01 CHAIN a BASE 19 T RMS = 0.770843E-02 CHAIN a BASE 20 C RMS = 0.203374E-01 CHAIN a BASE 21 C RMS = 0.202103E-01 CHAIN a BASE 22 T RMS = 0.788903E-02 CHAIN a BASE 23 C RMS = 0.203348E-01 CHAIN a BASE 24 C RMS = 0.202002E-01 3.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN YOUR PIVOT POINT WAS: 0.000 1.808 0.000 Calculations Across a Basepair #Ch Base #Ch Base Buckle Prop Open Angle Shear Stretch Stagger Dist -------------------------------------------------------------------------------------------- 1a G 24a C 7.502 -1.569 4.066 7.663 -0.099 0.105 0.117 0.185 2a G 23a C -1.684 -6.569 5.197 6.779 -0.077 0.073 -0.043 0.115 3a A 22a T 0.901 -6.264 8.738 6.322 0.103 0.020 0.165 0.195 4a G 21a C 2.870 2.864 5.044 4.053 -0.050 0.093 0.079 0.132 5a G 20a C 1.458 -1.222 5.717 1.901 -0.090 0.091 -0.029 0.132 6a A 19a T 6.836 -4.667 6.826 8.272 0.104 -0.014 0.102 0.147 7a G 18a C 3.851 -2.231 3.910 4.450 0.014 0.104 0.043 0.114 8a A 17a T 4.483 -7.935 4.063 9.112 0.103 -0.008 0.026 0.107 9a A 16a T 6.971 -8.211 7.598 10.764 0.121 0.003 0.143 0.187 10a G 15a C 4.218 -3.153 4.752 5.264 -0.041 0.093 0.119 0.156 11a A 14a T 3.312 -10.411 3.813 10.923 0.165 -0.001 0.033 0.168 12a A 13a T 2.896 -3.128 2.534 4.263 0.236 0.033 0.065 0.247 THE NUMBER OF SAMPLES= 12 -------------------------------------------------------------------------------------------- MEAN= 3.634 -4.375 5.188 6.647 0.041 0.049 0.068 0.157 STANDARD DEVIATION= 2.569 3.537 1.700 2.689 0.107 0.046 0.062 0.040 3.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Calculations of Basepairs #Ch: #Ch #Ch: #Ch Tilt Roll Twist Angle Shift Slide Rise Dist ------------------------------------------------------------------------------------------------- 1a: 24a 2a: 23a 1.922 1.011 36.926 2.134 0.392 -0.782 3.083 3.205 2a: 23a 3a: 22a 1.078 -6.313 39.477 6.278 0.505 -0.596 2.987 3.088 3a: 22a 4a: 21a -1.080 -9.700 37.242 9.588 -0.226 -0.731 3.186 3.276 4a: 21a 5a: 20a 2.426 -7.085 38.556 7.349 0.071 -0.662 3.223 3.291 5a: 20a 6a: 19a 0.073 -5.201 39.622 5.098 0.034 -0.354 3.018 3.039 6a: 19a 7a: 18a -1.658 -2.139 36.123 2.661 -0.406 -0.981 3.047 3.227 7a: 18a 8a: 17a 1.091 -3.857 40.249 3.927 -0.098 -0.383 3.029 3.054 8a: 17a 9a: 16a -1.915 -2.155 37.010 2.833 0.084 -0.758 2.954 3.051 9a: 16a 10a: 15a -2.394 -0.629 36.229 2.434 -0.401 -0.801 3.003 3.134 10a: 15a 11a: 14a 1.591 -2.128 39.774 2.604 -0.147 -0.442 3.018 3.054 11a: 14a 12a: 13a -1.921 -4.487 38.519 4.790 -0.062 -0.680 3.031 3.107 THE NUMBER OF SAMPLES= 11 ------------------------------------------------------------------------------------------------- MEAN= -0.072 -3.880 38.157 4.518 -0.023 -0.652 3.053 3.139 STANDARD DEVIATION= 1.690 2.950 1.436 2.287 0.274 0.184 0.078 0.090 3.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Calculations of Adjacent Single Bases #Ch Base #Ch Base Tilt Roll Twist Angle Shift Slide Rise Dist -------------------------------------------------------------------------------------------- 1a G 2a G -1.178 -0.472 37.469 1.246 -0.672 -0.707 3.118 3.267 2a G 3a A 4.189 -6.476 41.079 7.548 -0.517 -0.596 3.155 3.252 3a A 4a G -0.020 -4.645 35.493 4.571 -1.474 -0.564 3.137 3.512 4a G 5a G 1.108 -8.402 39.065 8.311 -1.222 -0.559 3.248 3.515 5a G 6a A 3.387 -5.504 40.339 6.330 -1.064 -0.221 3.122 3.306 6a A 7a G -2.065 0.782 34.755 2.174 -1.525 -0.697 3.053 3.483 7a G 8a A 3.026 -5.196 40.412 5.889 -1.194 -0.246 3.125 3.354 8a A 9a A 1.893 -0.391 38.843 1.896 -0.882 -0.516 3.053 3.219 9a A 10a G -1.878 3.668 34.844 4.058 -1.499 -0.525 3.025 3.416 10a G 11a A 3.373 -4.404 39.275 5.440 -1.128 -0.303 3.114 3.326 11a A 12a A 0.080 0.081 37.986 0.112 -1.062 -0.500 3.075 3.291 13a T 14a T 3.823 -9.121 38.827 9.701 -0.942 -0.803 3.111 3.348 14a T 15a C 0.304 0.061 40.244 0.304 -0.840 -0.500 3.047 3.200 15a C 16a T 2.744 -5.011 37.389 5.612 -0.704 -0.958 3.088 3.309 16a T 17a T 5.488 -4.003 34.832 6.689 -1.064 -0.890 2.989 3.295 17a T 18a C 0.882 -2.579 40.051 2.670 -1.003 -0.436 3.032 3.223 18a C 19a T 1.157 -5.100 37.371 5.137 -0.725 -1.162 3.102 3.391 19a T 20a C 3.236 -5.051 38.838 5.884 -1.137 -0.357 2.962 3.192 20a C 21a C -3.678 -5.698 38.066 6.657 -1.365 -0.645 3.183 3.522 21a C 22a T 1.856 -14.833 38.914 14.661 -1.029 -0.749 3.266 3.505 22a T 23a C 1.941 -6.344 37.707 6.515 -1.536 -0.464 2.937 3.347 23a C 24a C -4.978 2.631 36.549 5.535 -1.454 -0.769 3.142 3.546 THE NUMBER OF SAMPLES= 22 -------------------------------------------------------------------------------------------- MEAN= 1.122 -3.909 38.107 5.315 -1.093 -0.599 3.095 3.355 STANDARD DEVIATION= 2.579 4.107 1.853 3.212 0.291 0.228 0.080 0.112 3.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Local Helical Calculations of Basepairs #Ch: #Ch #Ch: #Ch Incl Tip H-Twist DX DY DZ ------------------------------------------------------------------------------- 1a: 24a 2a: 23a 1.566 -2.979 36.990 -1.366 -0.365 3.076 2a: 23a 3a: 22a -9.083 -1.551 39.993 -0.170 -0.619 3.056 3a: 22a 4a: 21a -14.595 1.625 38.500 0.145 0.203 3.272 4a: 21a 5a: 20a -10.400 -3.561 39.276 -0.103 0.196 3.288 5a: 20a 6a: 19a -7.478 -0.105 39.962 0.061 -0.042 3.039 6a: 19a 7a: 18a -3.386 2.625 36.225 -1.284 0.425 3.115 7a: 18a 8a: 17a -5.473 -1.548 40.448 -0.134 0.261 3.048 8a: 17a 9a: 16a -3.330 2.959 37.122 -0.919 -0.373 2.985 9a: 16a 10a: 15a -0.993 3.780 36.313 -1.201 0.324 3.036 10a: 15a 11a: 14a -3.061 -2.288 39.863 -0.411 0.392 3.029 11a: 14a 12a: 13a -6.639 2.843 38.827 -0.489 -0.136 3.089 THE NUMBER OF SAMPLES= 11 ------------------------------------------------------------------------------- MEAN= -5.716 0.164 38.502 -0.534 0.024 3.094 STANDARD DEVIATION= 4.366 2.558 1.503 0.536 0.338 0.093 3.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Local Helical Calculations of Adjacent Single Bases #Ch Base #Ch Base Incl Tip H-Twist DX DY DZ -------------------------------------------------------------------------- 1a G 2a G -0.722 1.800 37.491 -1.038 -0.915 3.146 2a G 3a A -8.929 -5.776 41.797 -0.146 -0.638 3.141 3a A 4a G -7.456 0.032 35.796 -0.248 0.588 3.185 4a G 5a G -12.135 -1.600 39.974 0.193 0.113 3.258 5a G 6a A -7.752 -4.770 40.853 0.280 0.084 3.025 6a A 7a G 1.287 3.399 34.825 -1.280 0.434 3.122 7a G 8a A -7.313 -4.259 40.857 0.211 0.230 3.034 8a A 9a A -0.577 -2.789 38.891 -0.728 -0.262 3.011 9a A 10a G 6.004 3.074 35.087 -1.397 0.408 3.029 10a G 11a A -6.383 -4.889 39.665 0.058 0.240 3.021 11a A 12a A 0.123 -0.120 37.987 -0.778 -0.166 3.072 13a T 14a T -13.179 -5.524 40.067 -0.123 0.006 3.108 14a T 15a C 0.087 -0.433 40.246 -0.734 -0.554 3.040 15a C 16a T -7.619 -4.172 37.823 -0.839 -0.373 3.128 16a T 17a T -6.503 -8.916 35.488 -0.913 0.688 2.869 17a T 18a C -3.684 -1.259 40.144 -0.351 -0.250 3.031 18a C 19a T -7.768 -1.762 37.735 -1.134 -0.537 3.207 19a T 20a C -7.393 -4.736 39.299 0.031 0.242 2.879 20a C 21a C -8.487 5.478 38.665 -0.240 -0.220 3.358 21a C 22a T -20.851 -2.610 41.686 0.637 -0.150 3.270 22a T 23a C -9.542 -2.919 38.286 0.034 0.761 2.892 23a C 24a C 4.092 7.743 36.980 -1.572 -0.198 3.246 THE NUMBER OF SAMPLES= 22 -------------------------------------------------------------------------- MEAN= -5.668 -1.591 38.620 -0.458 -0.021 3.094 STANDARD DEVIATION= 5.977 3.914 2.029 0.598 0.436 0.126 3.DAT YOUR REFERENCE ATOM INPUT FILENAME IS- [MARLA.RNASTAT]BASES.INN Relative Positions of Bases with respect to Neighboring Basepairs Basepair-1 Basepair+1 #Ch #Ch #Ch #Ch Base Base Base Base #Ch Base Buckle Prop Open Angle Shear Stretch Stagger Dist Dev ---------------------------------------------------------------------------------------------------------------------- 1a: 24a 3a: 22a 2a G -0.351 0.515 1.346 0.623 -0.035 -0.042 0.052 0.076 G: C A: T 23a C -1.233 -7.086 3.880 7.191 -0.002 0.117 -0.078 0.141 TOTAL -1.584 -6.571 5.226 7.814 -0.038 0.075 -0.026 0.217 ACTUAL -1.684 -6.569 5.197 6.779 -0.077 0.073 -0.043 0.115 0.132 2a: 23a 4a: 21a 3a A 1.671 -1.402 5.463 2.181 0.500 0.072 -0.018 0.505 G: C G: C 22a T -0.573 -4.938 3.198 4.970 -0.430 -0.086 0.193 0.479 TOTAL 1.098 -6.340 8.661 7.151 0.070 -0.015 0.175 0.985 ACTUAL 0.901 -6.264 8.738 6.322 0.103 0.020 0.165 0.195 0.567 3a: 22a 5a: 20a 4a G -0.410 0.101 1.848 0.422 -0.141 0.006 -0.036 0.146 A: T G: C 21a C 3.236 2.826 3.184 4.296 0.111 0.094 0.053 0.155 TOTAL 2.827 2.927 5.032 4.718 -0.030 0.100 0.017 0.301 ACTUAL 2.870 2.864 5.044 4.053 -0.050 0.093 0.079 0.132 0.214 4a: 21a 6a: 19a 5a G 1.927 -1.629 2.317 2.523 0.032 -0.121 0.094 0.157 G: C A: T 20a C -0.525 0.339 3.400 0.624 -0.112 0.212 -0.083 0.253 TOTAL 1.403 -1.290 5.716 3.147 -0.080 0.090 0.011 0.411 ACTUAL 1.458 -1.222 5.717 1.901 -0.090 0.091 -0.029 0.132 0.203 5a: 20a 7a: 18a 6a A 4.307 -3.891 5.187 5.802 0.325 0.309 -0.017 0.449 G: C G: C 19a T 2.505 -0.726 1.697 2.608 -0.259 -0.341 0.119 0.445 TOTAL 6.812 -4.617 6.884 8.411 0.066 -0.032 0.101 0.893 ACTUAL 6.836 -4.667 6.826 8.272 0.104 -0.014 0.102 0.147 0.533 6a: 19a 8a: 17a 7a G 0.492 -0.239 -0.106 0.547 -0.103 -0.259 -0.018 0.279 A: T A: T 18a C 3.349 -2.012 4.015 3.906 0.173 0.368 0.029 0.407 TOTAL 3.841 -2.252 3.909 4.453 0.070 0.109 0.010 0.687 ACTUAL 3.851 -2.231 3.910 4.450 0.014 0.104 0.043 0.114 0.466 7a: 18a 9a: 16a 8a A 3.846 -4.844 3.612 6.184 -0.026 0.193 0.038 0.199 G: C A: T 17a T 0.719 -3.083 0.378 3.166 0.086 -0.198 0.035 0.218 TOTAL 4.564 -7.927 3.990 9.349 0.060 -0.004 0.073 0.417 ACTUAL 4.483 -7.935 4.063 9.112 0.103 -0.008 0.026 0.107 0.233 8a: 17a 10a: 15a 9a A 3.722 -4.892 4.205 6.145 0.372 0.010 -0.016 0.372 A: T G: C 16a T 3.225 -3.312 3.424 4.622 -0.267 -0.029 0.146 0.306 TOTAL 6.947 -8.204 7.629 10.768 0.105 -0.019 0.130 0.678 ACTUAL 6.971 -8.211 7.598 10.764 0.121 0.003 0.143 0.187 0.306 9a: 16a 11a: 14a 10a G 0.031 -0.790 0.618 0.790 -0.101 -0.137 -0.011 0.170 A: T A: T 15a C 4.170 -2.342 4.162 4.782 0.110 0.235 0.074 0.270 TOTAL 4.201 -3.132 4.780 5.572 0.009 0.099 0.062 0.440 ACTUAL 4.218 -3.153 4.752 5.264 -0.041 0.093 0.119 0.156 0.274 10a: 15a 12a: 13a 11a A 3.531 -3.997 2.437 5.333 0.069 0.131 0.009 0.149 G: C A: T 14a T -0.122 -6.455 1.174 6.456 0.079 -0.133 0.078 0.173 TOTAL 3.410 -10.452 3.611 11.789 0.148 -0.001 0.087 0.322 ACTUAL 3.312 -10.411 3.813 10.923 0.165 -0.001 0.033 0.168 0.173