ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.10.1_2155精密化 | PDB_EXTRACT | 3.22 | データ抽出 | XDS | | データ削減 | XSCALE | | データスケーリング | autoSHARP | | 位相決定 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.499→37.982 Å / SU ML: 0.15 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 17.91
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1923 | 3348 | 5 % |
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Rwork | 0.1573 | - | - |
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obs | 0.1591 | 66950 | 97.83 % |
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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 |
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原子変位パラメータ | Biso max: 109.69 Å2 / Biso mean: 22.2694 Å2 / Biso min: 5.99 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.499→37.982 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3633 | 0 | 46 | 474 | 4153 |
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Biso mean | - | - | 40.72 | 31.05 | - |
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残基数 | - | - | - | - | 459 |
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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_d0.013 | 3826 | X-RAY DIFFRACTION | f_angle_d1.24 | 5187 | X-RAY DIFFRACTION | f_chiral_restr0.102 | 538 | X-RAY DIFFRACTION | f_plane_restr0.008 | 683 | X-RAY DIFFRACTION | f_dihedral_angle_d19.004 | 1440 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.4989-1.5204 | 0.2413 | 135 | 0.2389 | 2572 | 2707 | 94 | 1.5204-1.5431 | 0.2563 | 135 | 0.2199 | 2553 | 2688 | 96 | 1.5431-1.5672 | 0.2426 | 136 | 0.2179 | 2592 | 2728 | 95 | 1.5672-1.5929 | 0.2553 | 137 | 0.205 | 2594 | 2731 | 96 | 1.5929-1.6203 | 0.2279 | 140 | 0.1974 | 2671 | 2811 | 97 | 1.6203-1.6498 | 0.2454 | 136 | 0.1836 | 2590 | 2726 | 97 | 1.6498-1.6815 | 0.2336 | 139 | 0.1795 | 2627 | 2766 | 97 | 1.6815-1.7158 | 0.2262 | 139 | 0.1696 | 2653 | 2792 | 97 | 1.7158-1.7532 | 0.1946 | 139 | 0.1679 | 2627 | 2766 | 97 | 1.7532-1.7939 | 0.1904 | 141 | 0.1622 | 2687 | 2828 | 98 | 1.7939-1.8388 | 0.1915 | 137 | 0.1592 | 2600 | 2737 | 98 | 1.8388-1.8885 | 0.1895 | 141 | 0.1539 | 2690 | 2831 | 98 | 1.8885-1.9441 | 0.1894 | 141 | 0.154 | 2667 | 2808 | 98 | 1.9441-2.0068 | 0.1956 | 139 | 0.1508 | 2635 | 2774 | 98 | 2.0068-2.0785 | 0.1849 | 140 | 0.1441 | 2659 | 2799 | 98 | 2.0785-2.1618 | 0.1897 | 141 | 0.1467 | 2679 | 2820 | 98 | 2.1618-2.2601 | 0.1707 | 140 | 0.1425 | 2677 | 2817 | 99 | 2.2601-2.3793 | 0.1749 | 140 | 0.1558 | 2660 | 2800 | 99 | 2.3793-2.5283 | 0.1893 | 142 | 0.1632 | 2689 | 2831 | 99 | 2.5283-2.7235 | 0.198 | 141 | 0.1696 | 2671 | 2812 | 99 | 2.7235-2.9975 | 0.1773 | 143 | 0.1664 | 2724 | 2867 | 99 | 2.9975-3.4309 | 0.1913 | 141 | 0.1515 | 2672 | 2813 | 100 | 3.4309-4.3217 | 0.1569 | 142 | 0.1215 | 2709 | 2851 | 100 | 4.3217-37.9946 | 0.2012 | 143 | 0.1488 | 2704 | 2847 | 100 |
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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 | 0.7718 | 0.5956 | 1.32 | 0.4057 | 1.003 | 2.3185 | 0.1019 | -0.0506 | -0.0265 | 0.1174 | 0.0076 | 0.0453 | -0.0449 | 0.2342 | -0.0831 | 0.1367 | -0.01 | 0.0155 | 0.1556 | -0.0165 | 0.1113 | 18.6321 | -0.5212 | 55.1561 | 2 | 2.5091 | -0.0696 | 0.182 | 2.3056 | -0.3101 | 3.1065 | -0.0076 | -0.1444 | 0.2898 | 0.1595 | 0.074 | 0.2598 | -0.1183 | -0.1768 | -0.0106 | 0.0822 | -0.0043 | 0.0201 | 0.0697 | -0.0029 | 0.1117 | 12.7738 | 10.6264 | 84.1727 | 3 | 3.8421 | -0.2341 | 0.208 | 3.2787 | 0.7371 | 2.7286 | 0.0613 | 0.234 | 0.081 | -0.2219 | 0.0232 | 0.0941 | 0.1835 | 0.0103 | -0.0707 | 0.0851 | -0.0315 | 0.0086 | 0.0714 | 0.0333 | 0.0672 | 19.2669 | 8.6525 | 75.4305 | 4 | 2.1148 | 2.676 | -0.1344 | 4.7054 | 0.0005 | 2.0154 | 0.012 | -0.4922 | -0.3234 | -0.0612 | -0.0805 | -0.401 | 0.0662 | 0.2798 | 0.0326 | 0.1052 | 0.0038 | -0.0038 | 0.1723 | 0.0414 | 0.1141 | 21.2337 | 2.3852 | 89.7919 | 5 | 8.0174 | -5.8129 | -7.1428 | 6.5825 | 7.5873 | 9.2636 | 0.1447 | -0.1246 | 0.0565 | 0.1176 | -0.1843 | -0.0502 | -0.1593 | -0.1523 | -0.0699 | 0.1287 | -0.0227 | -0.0372 | 0.123 | 0.012 | 0.1692 | 31.4756 | 9.966 | 52.8864 | 6 | 3.4179 | -0.4284 | -0.5267 | 3.2037 | 1.2444 | 3.354 | 0.0611 | -0.5961 | -0.1377 | 0.6933 | 0.1034 | -0.1948 | -0.0136 | 0.4056 | -0.1886 | 0.2199 | -0.0353 | -0.0238 | 0.1687 | 0.0283 | 0.1144 | 29.0889 | 23.3329 | 83.2609 | 7 | 5.4507 | -1.2007 | -3.3819 | 5.8174 | 4.2984 | 7.28 | 0.1301 | -0.4979 | 0.1462 | 0.0838 | 0.0193 | -0.2179 | -0.2383 | 0.5851 | -0.1658 | 0.0885 | -0.0585 | -0.0099 | 0.1494 | 0.015 | 0.1053 | 33.3095 | 29.5293 | 79.138 | 8 | 3.9298 | 0.7006 | 0.1207 | 2.5563 | 0.433 | 0.7687 | 0.0441 | -0.0916 | 0.1197 | -0.194 | 0.0013 | -0.0994 | -0.2736 | 0.3726 | 0.0012 | 0.1002 | -0.0372 | 0.0066 | 0.0998 | -0.0129 | 0.0936 | 29.9249 | 28.6457 | 72.2646 | 9 | 5.9315 | 0.4457 | 4.2749 | 3.8352 | -0.6089 | 5.5628 | 0.2004 | 0.1412 | -0.7 | -0.1983 | 0.1788 | -0.7362 | 0.7102 | 0.8035 | -0.1809 | 0.1258 | 0.034 | 0.0507 | 0.1771 | -0.0304 | 0.3286 | 36.3446 | 16.4891 | 69.5488 | 10 | 3.1655 | 0.4551 | 0.5111 | 1.9371 | -0.3869 | 3.8925 | -0.0106 | 0.0533 | -0.0617 | -0.078 | 0.0395 | 0.0729 | -0.0909 | -0.2478 | -0.0173 | 0.0497 | -0.0177 | 0.017 | 0.0542 | -0.008 | 0.0754 | 21.2396 | 23.4193 | 70.1951 | 11 | 3.4319 | 3.524 | 1.97 | 6.006 | 3.0511 | 5.8412 | 0.0192 | -0.089 | 0.7838 | -0.3239 | -0.0913 | 0.2875 | -0.5956 | -0.0985 | -0 | 0.1908 | -0.0049 | -0.0266 | 0.0824 | -0.0013 | 0.2256 | 23.458 | 36.4121 | 73.111 | 12 | 0.766 | -1.4625 | -0.6871 | 5.182 | 2.2577 | 0.9412 | 0.1732 | 0.0413 | -0.015 | -0.1484 | -0.3279 | -0.0369 | 0.1759 | -0.212 | 0.1034 | 0.1396 | 0.0031 | 0.0194 | 0.145 | 0.0147 | 0.1331 | 29.5943 | 7.2348 | 70.7693 | 13 | 3.0231 | 0.0375 | 0.2152 | 2.7725 | 0.1415 | 1.9485 | 0.0557 | 0.2384 | -0.0905 | -0.3049 | -0.0668 | -0.1843 | 0.1505 | 0.2949 | 0.0123 | 0.1055 | 0.0391 | 0.0175 | 0.117 | -0.0024 | 0.0725 | 36.251 | -9.096 | 45.844 | 14 | 3.5923 | -0.5152 | 0.1072 | 3.3969 | -0.2731 | 3.896 | 0.0465 | -0.3726 | 0.0802 | 0.2592 | -0.0038 | 0.0519 | -0.0838 | -0.1294 | -0.0474 | 0.0651 | 0.032 | -0.0184 | 0.1087 | -0.0028 | 0.0742 | 29.6535 | -3.4407 | 52.5365 | 15 | 4.8083 | -3.363 | 4.6182 | 7.2457 | 0.0088 | 7.6926 | 0.2014 | -0.289 | -0.4465 | -0.4624 | -0.0923 | 0.4683 | 0.4055 | -0.5773 | -0.1837 | 0.1635 | -0.0161 | -0.0113 | 0.1084 | 0.0189 | 0.1862 | 28.3656 | -18.7491 | 47.9984 | 16 | 4.764 | -1.3888 | -5.9053 | 0.4408 | 1.8993 | 7.7988 | 0.0089 | -0.1978 | 0.0568 | -0.0196 | 0.1859 | -0.015 | 0.1214 | 0.2805 | -0.146 | 0.1748 | -0.0021 | -0.042 | 0.1385 | 0.0029 | 0.2 | 16.7276 | 17.0759 | 65.2748 | 17 | 3.2857 | 0.0156 | -0.7456 | 0.787 | -1.2724 | 2.1178 | 0.1229 | 0.4837 | -0.5219 | -0.5029 | -0.1433 | -0.0217 | 0.4839 | -0.3208 | -0.0289 | 0.2759 | 0.0422 | -0.0239 | 0.1589 | -0.06 | 0.1468 | 19.7521 | -0.6309 | 35.8747 | 18 | 2.6539 | -0.1974 | 0.0735 | 2.5461 | 0.2364 | 2.9432 | 0.0846 | 0.1629 | 0.0791 | -0.1986 | -0.0697 | 0.0408 | -0.2448 | -0.1402 | -0.0081 | 0.0946 | 0.0349 | -0.0011 | 0.0895 | 0.0122 | 0.0655 | 19.7641 | 9.0933 | 40.6761 | 19 | 2.8847 | 0.5942 | 2.8511 | 8.0977 | 0.1992 | 2.97 | -0.1192 | -0.0886 | 0.103 | 0.3153 | 0.0596 | -0.0461 | -0.4665 | 0.2553 | 0.0912 | 0.1797 | 0.0383 | 0.0112 | 0.2083 | 0.0313 | 0.0997 | 26.4002 | 15.3199 | 32.0963 |
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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 76 through 88 )A76 - 88 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 89 through 147 )A89 - 147 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 148 through 179 )A148 - 179 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 180 through 190 )A180 - 190 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 76 through 88 )B76 - 88 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 89 through 104 )B89 - 104 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 105 through 120 )B105 - 120 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 121 through 147 )B121 - 147 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 148 through 156 )B148 - 156 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 157 through 179 )B157 - 179 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 180 through 189 )B180 - 189 | 12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 76 through 88 )C76 - 88 | 13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 89 through 147 )C | | | | | | | | | | | | | | | | | | | | | | | | | |
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