ソフトウェア | 名称 | バージョン | 分類 | NB |
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MLPHARE | CCP4_5.99位相決定 | | HKL-2000 | | データ収集 | | HKL-2000 | | データ削減 | | HKL-2000 | | データスケーリング | | REFMAC | 5.2.0019精密化 | | | |
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精密化 | 構造決定の手法: 多重同系置換・異常分散 / 解像度: 1.7→55.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.209 / WRfactor Rwork: 0.168 / SU B: 4.56 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.113 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.21 | 1229 | 5 % | RANDOM |
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Rwork | 0.168 | - | - | - |
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all | 0.17 | 24792 | - | - |
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obs | 0.17 | 24792 | 88.8 % | - |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 21.165 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.46 Å2 | 0 Å2 | -0.57 Å2 |
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2- | - | -1.77 Å2 | 0 Å2 |
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3- | - | - | 2.22 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.113 Å | 0.112 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.7→55.64 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1796 | 0 | 0 | 211 | 2007 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.015 | 0.021 | 1942 | X-RAY DIFFRACTION | r_angle_refined_deg1.678 | 1.965 | 2665 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.615 | 5 | 266 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.093 | 22.609 | 92 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.919 | 15 | 336 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg17.458 | 15 | 23 | X-RAY DIFFRACTION | r_chiral_restr0.121 | 0.2 | 299 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.02 | 1515 | X-RAY DIFFRACTION | r_nbd_refined0.215 | 0.2 | 786 | X-RAY DIFFRACTION | r_nbtor_refined0.306 | 0.2 | 1307 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.121 | 0.2 | 191 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.25 | 0.2 | 52 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.192 | 0.2 | 12 | X-RAY DIFFRACTION | r_mcbond_it1.005 | 1.5 | 1247 | X-RAY DIFFRACTION | r_mcangle_it1.495 | 2 | 1971 | X-RAY DIFFRACTION | r_scbond_it2.142 | 3 | 780 | X-RAY DIFFRACTION | r_scangle_it3.255 | 4.5 | 676 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.699-1.743 | 0.368 | 41 | 0.278 | 867 | 2062 | 44.035 | 1.743-1.79 | 0.268 | 60 | 0.242 | 1121 | 1984 | 59.526 | 1.79-1.842 | 0.305 | 79 | 0.216 | 1357 | 1965 | 73.079 | 1.842-1.899 | 0.223 | 70 | 0.197 | 1451 | 1858 | 81.862 | 1.899-1.961 | 0.21 | 70 | 0.181 | 1619 | 1885 | 89.602 | 1.961-2.03 | 0.248 | 72 | 0.167 | 1630 | 1758 | 96.815 | 2.03-2.106 | 0.239 | 88 | 0.171 | 1587 | 1714 | 97.725 | 2.106-2.192 | 0.2 | 75 | 0.163 | 1610 | 1692 | 99.586 | 2.192-2.289 | 0.199 | 85 | 0.171 | 1460 | 1547 | 99.871 | 2.289-2.401 | 0.22 | 76 | 0.171 | 1433 | 1511 | 99.868 | 2.401-2.531 | 0.191 | 76 | 0.181 | 1409 | 1485 | 100 | 2.531-2.684 | 0.217 | 69 | 0.176 | 1273 | 1342 | 100 | 2.684-2.869 | 0.225 | 60 | 0.165 | 1194 | 1254 | 100 | 2.869-3.098 | 0.207 | 65 | 0.158 | 1145 | 1210 | 100 | 3.098-3.392 | 0.216 | 55 | 0.15 | 1050 | 1105 | 100 | 3.392-3.791 | 0.172 | 50 | 0.145 | 944 | 994 | 100 | 3.791-4.374 | 0.185 | 50 | 0.142 | 848 | 898 | 100 | 4.374-5.349 | 0.173 | 40 | 0.149 | 699 | 739 | 100 | 5.349-7.53 | 0.261 | 33 | 0.194 | 547 | 580 | 100 | 7.53-55.641 | 0.197 | 15 | 0.209 | 319 | 335 | 99.701 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 20.3582 | 15.9816 | 0.7241 | 39.1015 | 17.01 | 10.2054 | -1.2201 | 2.1265 | 0.5145 | -1.8364 | 0.595 | 1.0638 | -0.8353 | 0.5753 | 0.6251 | 0.1277 | -0.0915 | -0.099 | 0.223 | 0.0027 | 0.0104 | -30.104 | 24.933 | 16.31 | 2 | 2.1616 | 2.6611 | 0.8674 | 3.5377 | 1.5424 | 1.2088 | -0.0344 | -0.06 | 0.2393 | 0.0487 | -0.1362 | 0.2364 | -0.0863 | -0.1586 | 0.1706 | 0.026 | -0.0014 | 0.0003 | 0.0517 | -0.0281 | 0.0649 | -19.951 | 35.657 | 27.865 | 3 | 20.9144 | 11.0983 | 3.6426 | 9.5872 | 3.3882 | 3.8569 | 0.1535 | -0.5382 | -0.5123 | -0.1003 | -0.2679 | -0.0789 | -0.1286 | -0.5956 | 0.1145 | 0.0034 | -0.0091 | 0.0076 | 0.1643 | 0.016 | -0.0398 | -26.697 | 19.067 | 27.075 | 4 | 32.1616 | 0.8358 | -18.6614 | 1.7174 | 3.303 | 19.2903 | 0.2535 | 0.7201 | 1.9511 | -0.6954 | 0.9579 | 0.5917 | -0.8377 | 0.2521 | -1.2114 | 0.1082 | -0.1197 | 0.0669 | 0.1338 | 0.0279 | 0.1141 | -8.28 | 25.449 | 20.492 | 5 | 7.0038 | -1.9773 | -8.683 | 1.0426 | 0.8746 | 33.6311 | -0.1833 | -0.213 | -0.5838 | 0.0168 | -0.1348 | 0.2033 | 0.7135 | 0.5317 | 0.3182 | -0.0068 | 0.0086 | 0.0227 | 0.0059 | 0.0053 | 0.0574 | -12.067 | 21.247 | 25.831 | 6 | 47.7324 | 9.2507 | 1.0865 | 5.7536 | -3.8749 | 16.7427 | -0.3386 | -0.7951 | -0.7204 | -0.0084 | 0.8761 | 0.3479 | 0.11 | -1.6206 | -0.5375 | -0.032 | -0.0255 | 0.0201 | 0.2661 | 0.1417 | 0.0116 | -29.117 | 16.679 | 33.193 | 7 | 1.1873 | 3.0174 | -2.2238 | 8.5875 | -5.8298 | 4.1998 | 0.0417 | -0.089 | -0.5219 | 0.564 | -0.5299 | -1.0206 | -0.3073 | 0.1156 | 0.4882 | 0.0445 | -0.0089 | -0.0482 | 0.047 | 0.0487 | 0.1298 | -13.871 | 21.883 | 36.702 | 8 | 9.9526 | 7.1336 | 0.2836 | 5.8129 | -0.1624 | 3.3647 | 0.2184 | -0.1382 | 0.4657 | 0.443 | -0.1877 | 0.2023 | -0.2299 | -0.2013 | -0.0306 | 0.0524 | -0.0037 | 0.0235 | 0.0377 | -0.0101 | 0.0276 | -20.321 | 28.822 | 34.861 | 9 | 3.2664 | 3.7217 | 1.9091 | 5.9186 | 2.8131 | 1.7992 | 0.0777 | 0.105 | -0.2524 | 0.0144 | -0.0632 | -0.3291 | -0.0032 | -0.0907 | -0.0145 | 0.0171 | -0.0294 | 0.0147 | 0.0654 | -0.0143 | 0.0307 | -16.747 | 27.511 | 25.042 | 10 | 12.4645 | 9.7501 | 6.0439 | 7.8628 | 4.1499 | 4.3462 | 0.036 | 0.1952 | -0.1084 | 0.0372 | 0.2281 | -0.2945 | 0.116 | 0.1792 | -0.2641 | 0.0266 | 0.0045 | 0.0085 | 0.0476 | -0.0174 | 0.0966 | -7.437 | 43.713 | 28.993 | 11 | 10.6182 | 5.9845 | -1.1535 | 3.3734 | -0.6786 | 1.7558 | 0.1618 | -0.3887 | -0.1731 | 0.0943 | -0.2538 | -0.0318 | -0.0493 | 0.1972 | 0.092 | 0.0292 | 0.0208 | 0.036 | 0.0692 | -0.0019 | 0.012 | 16.182 | 62.538 | 30.857 | 12 | 5.8272 | 9.2107 | -4.9564 | 14.8025 | -9.259 | 12.5389 | 0.2195 | -0.4088 | -0.1898 | 0.0646 | -0.3876 | -0.2207 | 0.5621 | 1.3304 | 0.1681 | -0.0117 | -0.0015 | 0.0472 | 0.221 | 0.0097 | -0.0214 | 23.338 | 67.282 | 19.491 | 13 | 3.5384 | 2.4799 | -0.3538 | 1.9364 | -0.5847 | 0.6071 | -0.026 | 0.023 | -0.2543 | -0.1012 | 0.0004 | -0.0809 | 0.0022 | 0.021 | 0.0256 | 0.0389 | 0.0045 | 0.0223 | 0.0461 | -0.0125 | 0.0966 | 5.239 | 53.697 | 27.263 | 14 | 7.408 | -7.4131 | -0.6493 | 8.6289 | -1.8095 | 5.0522 | 0.3098 | 0.5748 | 0.3472 | -0.0636 | -0.1087 | 0.1979 | 0.0606 | -0.3548 | -0.2011 | 0.0121 | 0.0149 | -0.0301 | 0.0487 | 0.0485 | 0.085 | 4.007 | 67.465 | 21.116 | 15 | 24.1353 | 16.3241 | 0.9098 | 14.1706 | 1.1513 | 12.9513 | -1.192 | 1.8458 | -1.4118 | -2.2767 | 1.5166 | -0.47 | 0.2905 | 0.6527 | -0.3246 | 0.2942 | -0.0664 | 0.0416 | 0.1219 | -0.1187 | -0.0688 | 14.035 | 59.551 | 12.991 | 16 | 8.5736 | 10.6344 | -4.0542 | 13.2441 | -5.7798 | 12.4614 | -0.5903 | 0.1838 | -0.6435 | -1.1112 | -0.1259 | -0.3245 | 1.3021 | -0.1779 | 0.7162 | 0.1833 | -0.0125 | 0.0609 | -0.0282 | -0.0607 | 0.0152 | 11.566 | 53.502 | 19.82 | 17 | 3.3334 | 4.1396 | -1.7913 | 6.353 | -2.6175 | 1.09 | -0.028 | 0.0714 | -0.3732 | -0.0741 | -0.0814 | -0.2323 | -0.0885 | -0.0012 | 0.1094 | 0.0516 | -0.0014 | 0.0182 | 0.0465 | -0.0042 | 0.0782 | 7.116 | 47.332 | 27.108 | 18 | 2.9508 | 1.2241 | -0.6033 | 2.1421 | -0.6012 | 0.5014 | 0.0032 | 0.1016 | 0.2043 | -0.079 | -0.0029 | 0.1155 | -0.1023 | -0.0856 | -0.0003 | 0.0776 | 0.0054 | 0.0065 | 0.0397 | 0.0151 | 0.0222 | 10.992 | 69.512 | 24.595 | 19 | 11.5154 | 2.5175 | 2.1426 | 12.9538 | -3.6551 | 1.7695 | 0.1089 | 0.0298 | 0.2205 | 0.1778 | -0.0943 | -0.2168 | 0.1842 | -0.0257 | -0.0146 | -0.014 | -0.0131 | 0.0137 | 0.0509 | -0.0019 | 0.1023 | -11.154 | 51.567 | 26.569 | 20 | 12.3194 | 7.9718 | 0.5199 | 5.4374 | 0.6656 | 0.5395 | 0.0893 | -0.2289 | 0.2717 | 0.0201 | -0.1053 | 0.3072 | -0.1248 | 0.026 | 0.0159 | 0.0364 | 0.0057 | 0.0258 | 0.0447 | 0.019 | 0.0317 | 10.98 | 66.615 | 31.34 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A ID | Refine TLS-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | 1 - 4 | 1 - 4 | 2 | 2 | 5 - 27 | 5 - 27 | 3 | 3 | 28 - 35 | 28 - 35 | 4 | 4 | 36 - 42 | 36 - 42 | 5 | 5 | 43 - 48 | 43 - 48 | 6 | 6 | 49 - 56 | 49 - 56 | 7 | 7 | 57 - 70 | 57 - 70 | 8 | 8 | 71 - 82 | 71 - 82 | 9 | 9 | 83 - 108 | 83 - 108 | 10 | 10 | 109 - 118 | 109 - 118 | 11 | 11 | 119 - 130 | 119 - 130 | 12 | 12 | 131 - 136 | 131 - 136 | 13 | 13 | 137 - 154 | 137 - 154 | 14 | 14 | 155 - 163 | 155 - 163 | 15 | 15 | 164 - 171 | 164 - 171 | 16 | 16 | 172 - 176 | 172 - 176 | 17 | 17 | 177 - 192 | 177 - 192 | 18 | 18 | 193 - 209 | 193 - 209 | 19 | 19 | 210 - 218 | 210 - 218 | 20 | 20 | 219 - 231 | 219 - 231 |
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