ソフトウェア | 名称 | バージョン | 分類 |
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MAR345 | | データ収集 | REFMAC | 5.5 | 精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | REFMAC | 5.5 | 位相決定 |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: pdb entry 1TT0 解像度: 1.7→29.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.885 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.098 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.21631 | 3027 | 1 % | RANDOM |
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Rwork | 0.18019 | - | - | - |
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all | 0.18056 | 292517 | - | - |
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obs | 0.18056 | 292517 | 96.83 % | - |
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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: 12.274 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.87 Å2 | 0 Å2 | -0.44 Å2 |
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2- | - | -0.03 Å2 | 0 Å2 |
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3- | - | - | 0.89 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.7→29.3 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 18111 | 0 | 294 | 1900 | 20305 |
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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_d0.024 | 0.022 | 18882 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 16430 | X-RAY DIFFRACTION | r_angle_refined_deg2.071 | 1.963 | 25660 | X-RAY DIFFRACTION | r_angle_other_deg3.275 | 3 | 38387 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.997 | 5 | 2297 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.946 | 24.497 | 894 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.216 | 15 | 3021 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.744 | 15 | 108 | X-RAY DIFFRACTION | r_chiral_restr0.187 | 0.2 | 2784 | X-RAY DIFFRACTION | r_gen_planes_refined0.011 | 0.021 | 20915 | X-RAY DIFFRACTION | r_gen_planes_other0 | 0.02 | 3761 | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it1.253 | 1.5 | 11494 | X-RAY DIFFRACTION | r_mcbond_other0.441 | 1.5 | 4618 | X-RAY DIFFRACTION | r_mcangle_it2.039 | 2 | 18671 | X-RAY DIFFRACTION | r_scbond_it3.101 | 3 | 7388 | X-RAY DIFFRACTION | r_scangle_it4.756 | 4.5 | 6989 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.7→1.792 Å / Total num. of bins used: 10
| Rfactor | 反射数 | %反射 |
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Rfree | 0.302 | 432 | - |
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Rwork | 0.258 | 43138 | - |
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obs | - | - | 98.31 % |
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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 | 0.1744 | 0.0769 | 0.1032 | 0.353 | 0.0659 | 0.0778 | 0.0204 | -0.0053 | 0.0068 | 0.0025 | -0.0008 | -0.028 | 0.0348 | -0.0177 | -0.0196 | 0.1074 | -0.0032 | 0.0175 | 0.1025 | -0.0065 | 0.0844 | 18.042 | 46.227 | 127.636 | 2 | 0.5025 | -0.0646 | -0.1027 | 0.2728 | 0.1404 | 0.3626 | -0.0369 | -0.0214 | 0.0215 | 0.0494 | 0.0512 | -0.0931 | -0.0042 | 0.0578 | -0.0143 | 0.0869 | -0.0065 | -0.0039 | 0.0784 | -0.0219 | 0.1146 | 36.351 | 53.935 | 133.127 | 3 | 0.6094 | -0.1536 | -0.0871 | 0.7978 | 0.119 | 1.1599 | 0.0046 | 0.0002 | 0.0594 | -0.0154 | -0.0032 | 0.144 | -0.0812 | -0.1357 | -0.0014 | 0.0876 | 0.0154 | 0.0099 | 0.0849 | -0.0239 | 0.1234 | 11.434 | 62.115 | 133.143 | 4 | 0.7758 | -0.8541 | 0.1839 | 2.5358 | 0.2077 | 0.6296 | 0.0128 | 0.0521 | -0.0454 | 0.1671 | 0.1052 | -0.3353 | 0.0988 | 0.1102 | -0.1179 | 0.0648 | 0.0001 | -0.0188 | 0.0877 | -0.0556 | 0.1539 | 49.318 | 37.533 | 116.904 | 5 | 0.375 | -0.0013 | -0.1267 | 0.3379 | 0.1509 | 0.3739 | 0.0085 | 0.0256 | 0.0824 | -0.0171 | 0.0169 | -0.0116 | -0.0583 | -0.0122 | -0.0254 | 0.0853 | 0.0002 | 0.0172 | 0.0655 | -0.0077 | 0.0888 | 25.358 | 61.206 | 124.131 | 6 | 0.2355 | 0.0336 | -0.092 | 0.2341 | -0.0252 | 0.3802 | 0.0289 | -0.0105 | -0.031 | 0.0027 | 0.016 | -0.0202 | -0.0146 | 0.0452 | -0.0449 | 0.091 | -0.0026 | -0.0036 | 0.0861 | -0.0044 | 0.0838 | 27.842 | 23.874 | 128.858 | 7 | 0.6328 | -0.1097 | 0.2184 | 0.2616 | -0.1256 | 0.3453 | -0.0014 | -0.0631 | -0.0566 | 0.0434 | 0.0226 | 0.0227 | 0.0189 | -0.0579 | -0.0213 | 0.0984 | -0.004 | 0.0203 | 0.0875 | 0.0135 | 0.0778 | 10.384 | 17.58 | 137.179 | 8 | 0.9458 | -0.1117 | 0.2537 | 1.0704 | -0.093 | 0.9854 | 0.0369 | -0.0088 | -0.057 | 0.0076 | -0.0397 | -0.1977 | 0.1017 | 0.1191 | 0.0028 | 0.086 | 0.0195 | -0.0004 | 0.092 | 0.0237 | 0.1273 | 35.065 | 8.585 | 136.327 | 9 | 0.7896 | -0.8337 | -0.0736 | 1.4582 | -0.1448 | 0.616 | 0.0338 | 0.018 | 0.0405 | -0.0092 | 0.0577 | 0.0837 | -0.0723 | -0.0761 | -0.0916 | 0.084 | -0.0001 | 0.0162 | 0.0943 | 0.0284 | 0.0888 | -4.275 | 31.911 | 119.976 | 10 | 0.4446 | -0.0921 | 0.3092 | 0.2833 | -0.1698 | 0.4646 | 0.0512 | 0.0057 | -0.095 | -0.0049 | 0.002 | -0.0219 | 0.0483 | 0.014 | -0.0531 | 0.0892 | 0.0038 | -0.0003 | 0.0678 | -0.0001 | 0.0781 | 19.921 | 8.615 | 128.251 | 11 | 0.2048 | 0.1132 | 0.238 | 0.2562 | 0.2388 | 0.3377 | -0.0211 | 0.0836 | -0.0069 | -0.1101 | 0.0451 | -0.0315 | -0.0826 | 0.1075 | -0.024 | 0.1438 | -0.0187 | 0.0215 | 0.1255 | 0.0047 | 0.0091 | 9.799 | 37.185 | 79.951 | 12 | 0.2683 | -0.0565 | 0.1333 | 0.5239 | -0.1091 | 0.7071 | 0.0264 | 0.067 | -0.0497 | -0.129 | 0.0108 | 0.0453 | 0.0692 | 0.0083 | -0.0372 | 0.1226 | -0.011 | -0.0113 | 0.111 | -0.0229 | 0.0141 | 0.661 | 19.725 | 74.408 | 13 | 0.7397 | -0.0529 | 0.0566 | 0.8066 | -0.0338 | 2.0159 | -0.0173 | 0.0288 | 0.1513 | -0.1084 | 0.0329 | 0.0155 | -0.2788 | -0.1278 | -0.0156 | 0.171 | 0.0083 | -0.029 | 0.0852 | 0.0164 | 0.0391 | -5.64 | 44.619 | 73.585 | 14 | 0.7351 | -0.0212 | 0.196 | 1.0311 | 0.093 | 0.7931 | 0.0171 | 0.1228 | -0.0697 | -0.0542 | 0.0457 | -0.1944 | 0.1593 | 0.1212 | -0.0627 | 0.1566 | 0.0197 | -0.0026 | 0.1347 | -0.0481 | 0.0671 | 16.208 | 5.232 | 91.761 | 15 | 0.1138 | -0.0304 | 0.0871 | 0.2512 | -0.0978 | 0.5671 | 0.0057 | 0.0314 | 0.0147 | -0.065 | 0.0404 | 0.0492 | -0.0474 | -0.0557 | -0.0461 | 0.1228 | 0.0001 | -0.0191 | 0.1164 | 0.0105 | 0.0436 | -5.946 | 31.193 | 82.749 | 16 | 2.7443 | 0.6553 | 1.4186 | 1.6021 | -0.7654 | 3.5698 | -0.0257 | 1.1744 | -0.428 | -0.3617 | 0.368 | -0.1185 | 0.244 | 0.4777 | -0.3424 | 0.2411 | -0.1496 | 0.1248 | 0.8973 | -0.3313 | 0.1765 | 36.242 | 27.399 | 61.265 | 17 | 0.4598 | 0.3301 | 0.0078 | 0.393 | 0.0887 | 0.0502 | -0.0278 | 0.1248 | -0.0596 | -0.0561 | 0.0875 | -0.1314 | -0.0261 | 0.0198 | -0.0597 | 0.1045 | -0.0008 | 0.047 | 0.1643 | -0.0566 | 0.0803 | 26.778 | 24.687 | 89.857 | 18 | 1.2599 | 0.1008 | 0.2032 | 0.8789 | 0.3667 | 0.5358 | -0.0715 | 0.6443 | -0.1637 | -0.2117 | 0.1893 | -0.2288 | -0.1095 | 0.267 | -0.1178 | 0.1508 | -0.0827 | 0.1191 | 0.4457 | -0.1317 | 0.1108 | 40.829 | 34.623 | 72.994 | 19 | 2.1033 | -1.5151 | 0.7082 | 1.7478 | -0.1263 | 1.0639 | -0.1182 | 0.2733 | 0.0948 | -0.1918 | 0.0291 | -0.0057 | -0.2596 | 0.0341 | 0.0891 | 0.2275 | -0.0714 | 0.0415 | 0.1877 | 0.0494 | 0.0721 | 24.677 | 61.504 | 85.405 | 20 | 1.1928 | 0.1843 | 0.3677 | 0.4566 | 0.2281 | 0.4221 | -0.0892 | 0.512 | -0.1394 | -0.1155 | 0.2133 | -0.2272 | -0.0376 | 0.2796 | -0.1241 | 0.0945 | -0.0584 | 0.0969 | 0.336 | -0.126 | 0.1389 | 45.293 | 33.605 | 80.994 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A43 - 159 | 2 | X-RAY DIFFRACTION | 2 | A160 - 293 | 3 | X-RAY DIFFRACTION | 3 | A294 - 358 | 4 | X-RAY DIFFRACTION | 4 | A359 - 476 | 5 | X-RAY DIFFRACTION | 5 | A477 - 618 | 6 | X-RAY DIFFRACTION | 6 | B43 - 157 | 7 | X-RAY DIFFRACTION | 7 | B158 - 293 | 8 | X-RAY DIFFRACTION | 8 | B294 - 357 | 9 | X-RAY DIFFRACTION | 9 | B358 - 474 | 10 | X-RAY DIFFRACTION | 10 | B475 - 618 | 11 | X-RAY DIFFRACTION | 11 | C45 - 158 | 12 | X-RAY DIFFRACTION | 12 | C159 - 293 | 13 | X-RAY DIFFRACTION | 13 | C294 - 359 | 14 | X-RAY DIFFRACTION | 14 | C360 - 473 | 15 | X-RAY DIFFRACTION | 15 | C474 - 619 | 16 | X-RAY DIFFRACTION | 16 | D45 - 85 | 17 | X-RAY DIFFRACTION | 17 | D86 - 149 | 18 | X-RAY DIFFRACTION | 18 | D150 - 370 | 19 | X-RAY DIFFRACTION | 19 | D371 - 461 | 20 | X-RAY DIFFRACTION | 20 | D462 - 618 | | | | | | | | | | | | | | | | | | | | |
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