ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.11.1_2575: ???)精密化 | HKL-2000 | | データ削減 | SCALEPACK | | データスケーリング | MOLREP | | 位相決定 | |
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精密化 | 解像度: 1.7→22.458 Å / SU ML: 0.21 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 22.83 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2125 | 2689 | 5.1 % |
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Rwork | 0.1763 | - | - |
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obs | 0.1782 | 52746 | 81.47 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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精密化ステップ | サイクル: LAST / 解像度: 1.7→22.458 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4431 | 0 | 0 | 591 | 5022 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.006 | 4549 | X-RAY DIFFRACTION | f_angle_d0.832 | 6205 | X-RAY DIFFRACTION | f_dihedral_angle_d3.016 | 2993 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 704 | X-RAY DIFFRACTION | f_plane_restr0.005 | 794 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.7002-1.7311 | 0.2768 | 135 | 0.2339 | 2736 | X-RAY DIFFRACTION | 84 | 1.7311-1.7643 | 0.2771 | 142 | 0.2337 | 2734 | X-RAY DIFFRACTION | 85 | 1.7643-1.8003 | 0.2714 | 137 | 0.2211 | 2746 | X-RAY DIFFRACTION | 84 | 1.8003-1.8395 | 0.2934 | 133 | 0.2158 | 2645 | X-RAY DIFFRACTION | 82 | 1.8395-1.8822 | 0.2601 | 138 | 0.2059 | 2625 | X-RAY DIFFRACTION | 81 | 1.8822-1.9293 | 0.2338 | 136 | 0.2059 | 2495 | X-RAY DIFFRACTION | 78 | 1.9293-1.9814 | 0.2321 | 134 | 0.201 | 2449 | X-RAY DIFFRACTION | 76 | 1.9814-2.0397 | 0.2516 | 126 | 0.202 | 2463 | X-RAY DIFFRACTION | 76 | 2.0397-2.1055 | 0.2373 | 156 | 0.2004 | 2442 | X-RAY DIFFRACTION | 77 | 2.1055-2.1807 | 0.2499 | 151 | 0.1929 | 2429 | X-RAY DIFFRACTION | 76 | 2.1807-2.2679 | 0.2471 | 133 | 0.1943 | 2592 | X-RAY DIFFRACTION | 80 | 2.2679-2.371 | 0.2534 | 142 | 0.189 | 2590 | X-RAY DIFFRACTION | 80 | 2.371-2.4959 | 0.2403 | 148 | 0.1923 | 2622 | X-RAY DIFFRACTION | 82 | 2.4959-2.652 | 0.2281 | 132 | 0.191 | 2695 | X-RAY DIFFRACTION | 83 | 2.652-2.8564 | 0.2251 | 157 | 0.1875 | 2712 | X-RAY DIFFRACTION | 84 | 2.8564-3.1432 | 0.2063 | 140 | 0.1773 | 2567 | X-RAY DIFFRACTION | 80 | 3.1432-3.5964 | 0.1821 | 143 | 0.1611 | 2656 | X-RAY DIFFRACTION | 82 | 3.5964-4.525 | 0.1818 | 153 | 0.1396 | 2832 | X-RAY DIFFRACTION | 88 | 4.525-22.4596 | 0.1663 | 153 | 0.1542 | 3027 | X-RAY DIFFRACTION | 92 |
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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 | 5.8156 | 7.0383 | 5.0198 | 8.4852 | 6.1364 | 4.4287 | -0.337 | 0.5532 | 0.1699 | -0.3299 | 0.207 | 0.1249 | -0.1184 | 0.1487 | 0.2133 | 0.2518 | -0.0035 | 0.0355 | 0.297 | -0.0026 | 0.2985 | -3.8625 | -40.6108 | 6.0906 | 2 | 5.5404 | 2.9561 | 4.0951 | 3.0173 | 2.4457 | 3.7414 | 0.0319 | 0.0488 | -0.4957 | 0.0508 | 0.1812 | -0.3907 | -0.0071 | 0.0944 | -0.2379 | 0.1646 | 0.0155 | 0.0192 | 0.1833 | 0.0171 | 0.2539 | -9.7657 | -46.2515 | 8.6904 | 3 | 3.1931 | -1.9717 | 4.333 | 3.0625 | -2.4704 | 5.929 | -0.469 | -0.6539 | 0.49 | 0.1796 | 0.4364 | 0.4533 | -0.4201 | -0.7924 | 0.1335 | 0.2334 | 0.0224 | 0.0001 | 0.25 | 0.0281 | 0.301 | -23.1943 | -37.969 | 8.6757 | 4 | 3.0167 | -0.5894 | 4.6822 | 1.5445 | -0.3407 | 7.8024 | 0.1567 | 0.0376 | 0.0637 | 0.0867 | -0.1186 | -0.0282 | -0.4646 | -0.059 | 0.0024 | 0.2609 | -0.0219 | 0.0049 | 0.1979 | 0.0546 | 0.2141 | -19.3978 | -43.0994 | 14.0243 | 5 | 2.2412 | 0.8773 | 0.7142 | 1.5545 | 0.1163 | 1.0516 | -0.1036 | -0.0666 | -0.2504 | -0.0637 | 0.1521 | 0.037 | -0.0053 | -0.0665 | -0.072 | 0.1581 | 0.0054 | 0.012 | 0.1691 | 0.0224 | 0.1932 | -17.4744 | -42.5972 | 7.2481 | 6 | 7.1581 | 0.6945 | 1.5419 | 2.1591 | 1.5696 | 4.021 | 0.2997 | 0.6081 | -1.0016 | -0.4202 | -0.1412 | 0.2909 | 0.1094 | -0.3116 | -0.0923 | 0.3506 | -0.0225 | -0.0707 | 0.2643 | -0.0678 | 0.4018 | -32.2136 | -52.6371 | -6.8629 | 7 | 4.3413 | 2.3566 | 3.8149 | 3.0794 | 2.4203 | 3.512 | -0.1261 | 0.0096 | -0.0452 | -0.1108 | 0.1123 | -0.116 | -0.209 | 0.1145 | -0.0101 | 0.1691 | 0.012 | 0.0363 | 0.1585 | 0.0016 | 0.1325 | -8.5691 | -33.1802 | 6.4787 | 8 | 1.5081 | 0.1886 | 0.0247 | 1.2753 | -1.3829 | 4.4561 | 0.0671 | -0.1361 | -0.0438 | -0.0645 | -0.1355 | -0.0633 | 0.0399 | 0.4172 | 0.0565 | 0.1414 | 0.0311 | 0.024 | 0.2101 | -0.0119 | 0.1907 | -1.0679 | -24.1807 | -12.0727 | 9 | 1.8431 | 0.5362 | -0.4105 | 2.5664 | 0.6076 | 1.0583 | 0.05 | 0.09 | -0.0114 | -0.2242 | 0.0521 | 0.0979 | -0.03 | -0.0653 | -0.0997 | 0.1785 | 0.0099 | 0.0113 | 0.1673 | -0.006 | 0.1004 | -11.4655 | -27.1717 | -12.3788 | 10 | 2.7602 | -0.5878 | 1.4489 | 2.3637 | -0.4881 | 4.5671 | 0.1492 | 0.0054 | -0.059 | -0.2656 | 0.0138 | -0.0996 | 0.3459 | 0.0338 | -0.1663 | 0.2164 | -0.0022 | 0.0212 | 0.1917 | -0.0221 | 0.1711 | -4.4533 | -30.369 | -16.6423 | 11 | 0.9198 | 0.3263 | -1.2364 | 1.3195 | -1.4478 | 2.7244 | 0.1122 | 0.0365 | 0.0018 | -0.0529 | -0.0454 | 0.061 | -0.1157 | 0.0756 | -0.0695 | 0.1998 | 0.0235 | 0.0009 | 0.1883 | -0.0041 | 0.1487 | -9.8047 | -22.2887 | -11.8837 | 12 | 0.8542 | -1.1044 | -0.2294 | 3.8124 | 0.383 | 1.6427 | 0.1258 | 0.0389 | 0.0979 | -0.3537 | -0.2103 | 0.0561 | -0.1894 | -0.0412 | 0.0842 | 0.1364 | -0.0103 | -0.0162 | 0.1966 | -0.026 | 0.1834 | -11.1108 | 3.7846 | -27.4186 | 13 | 0.9572 | -0.0035 | -0.121 | 2.096 | 0.6041 | 1.4383 | 0.0112 | -0.0582 | -0.0043 | -0.0406 | -0.0086 | 0.028 | 0.013 | 0.0789 | -0.0135 | 0.157 | 0.0226 | 0.005 | 0.1562 | -0.01 | 0.1588 | -11.1379 | 5.762 | -23.3056 | 14 | 3.4215 | -1.2266 | -1.1122 | 2.6607 | 2.9005 | 3.0108 | 0.0501 | 0.1383 | 0.1469 | -0.1973 | 0.1252 | -0.627 | -0.0581 | 0.2181 | -0.2394 | 0.2125 | -0.0109 | 0.0023 | 0.2175 | -0.0143 | 0.2497 | -3.1383 | 10.7591 | -26.2079 | 15 | 2.0786 | -0.3817 | -0.2207 | 5.9778 | 2.6428 | 3.1812 | 0.2552 | 0.1938 | -0.3999 | -0.6358 | -0.5326 | 0.6081 | -0.2538 | -0.5661 | 0.1886 | 0.2698 | 0.0298 | -0.0677 | 0.2914 | -0.0182 | 0.2876 | -28.9598 | -13.5922 | -7.8584 | 16 | 1.9595 | 0.9 | 0.3052 | 1.0211 | -0.7041 | 1.735 | -0.0132 | 0.1132 | -0.2177 | -0.0731 | 0.0534 | 0.1069 | 0.1988 | -0.1849 | -0.0281 | 0.1904 | 0.0139 | 0.0247 | 0.2336 | -0.0214 | 0.2636 | -29.8556 | -17.0465 | -0.9843 | 17 | 2.0467 | -0.7228 | -0.2442 | 3.0905 | -1.1243 | 2.9789 | 0.1292 | 0.0067 | 0.0143 | -0.0306 | -0.1164 | -0.1861 | -0.2869 | 0.0626 | -0.0174 | 0.1685 | 0.0225 | 0.034 | 0.1467 | 0.0022 | 0.1744 | -16.9719 | -16.9912 | -2.4529 | 18 | 0.8643 | -0.057 | -0.0254 | 2.1785 | 0.8109 | 1.5784 | 0.0128 | -0.1109 | -0.0546 | 0.1271 | -0.0645 | 0.0779 | 0.0268 | -0.126 | 0.0552 | 0.142 | -0.0049 | 0.0085 | 0.1609 | -0.0001 | 0.1583 | -23.79 | -19.8295 | 4.6436 | 19 | 0.9787 | -1.0054 | -0.6679 | 3.5358 | 1.6628 | 2.1246 | 0.1295 | 0.0181 | 0.0139 | -0.2332 | -0.1384 | -0.1988 | -0.1812 | -0.1427 | -0.0114 | 0.1716 | 0.0197 | 0.0174 | 0.1894 | 0.0078 | 0.1848 | -21.3294 | -12.1816 | -1.0067 | 20 | 0.6411 | 0.0422 | 0.0131 | 1.8337 | -0.4766 | 0.502 | 0.0842 | 0.0932 | -0.0195 | 0.185 | -0.1514 | 0.2767 | 0.0231 | -0.1437 | 0.0768 | 0.1719 | 0.0081 | 0.0142 | 0.1533 | -0.0061 | 0.1314 | -24.277 | -10.8484 | -8.3719 | 21 | 3.9312 | -2.1687 | -4.266 | 2.6256 | 4.2183 | 7.0509 | 0.2378 | 0.1264 | 0.1567 | -0.4318 | -0.0778 | -0.1689 | -0.3678 | 0.1187 | -0.1568 | 0.27 | 0.0301 | -0.0212 | 0.1937 | 0.035 | 0.2793 | -17.0416 | 12.303 | -33.3727 | 22 | 0.8189 | 0.6463 | -1.2241 | 1.2491 | 0.1638 | 8.9036 | -0.0897 | -0.0622 | 0.0061 | -0.1956 | 0.0204 | 0.3122 | 0.3486 | -0.1461 | 0.0924 | 0.2041 | 0.0271 | -0.0088 | 0.1378 | -0.0031 | 0.2889 | -26.6677 | 7.5963 | -22.7639 | 23 | 4.3053 | -0.6377 | 3.2432 | 1.4435 | -2.0517 | 7.4166 | -0.1478 | -0.0597 | 0.1481 | -0.2009 | 0.2282 | 0.3076 | -0.0777 | -0.5703 | -0.0614 | 0.2679 | -0.0097 | -0.0498 | 0.1893 | -0.0061 | 0.3446 | -29.2198 | 4.7143 | -31.1851 | 24 | 1.1115 | -0.0117 | -0.1331 | 2.5501 | -0.6185 | 9.5265 | -0.0284 | 0.0448 | 0.1099 | -0.0801 | -0.0849 | 0.0673 | 0.0417 | 0.1987 | 0.0821 | 0.1311 | 0.0144 | -0.0084 | 0.1228 | -0.0009 | 0.2177 | -21.4266 | 6.3669 | -24.7271 | 25 | 2.0316 | 0.2217 | -1.8787 | 2.4757 | -0.944 | 2.3653 | 0.2413 | 0.042 | 0.4075 | -0.0557 | 0.163 | 0.5072 | -0.3878 | -0.2423 | -0.512 | 0.1885 | 0.0408 | -0.0034 | 0.2026 | 0.0361 | 0.3892 | -30.4191 | 14.968 | -26.7982 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ( CHAIN A AND RESID 2:11 )A2 - 11 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 12:37 )A12 - 37 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 38:52 )A38 - 52 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN A AND RESID 53:62 )A53 - 62 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN A AND RESID 63:117 )A63 - 117 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN A AND RESID 118:139 )A118 - 139 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN A AND RESID 140:154 )A140 - 154 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN H AND RESID 1:33 )H1 - 33 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN H AND RESID 34:59 )H34 - 59 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN H AND RESID 60:82 )H60 - 82 | 11 | X-RAY DIFFRACTION | 11 | ( CHAIN H AND RESID 83:106 )H83 - 106 | 12 | X-RAY DIFFRACTION | 12 | ( CHAIN H AND RESID 107:134 )H107 - 134 | 13 | X-RAY DIFFRACTION | 13 | ( CHAIN H AND RESID 135:188 )H135 - 188 | 14 | X-RAY DIFFRACTION | 14 | ( CHAIN H AND RESID 189:214 )H189 - 214 | 15 | X-RAY DIFFRACTION | 15 | ( CHAIN L AND | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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