ソフトウェア | 名称 | バージョン | 分類 |
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XSCALE | | データスケーリング | PHASER | 2.5.6位相決定 | PHENIX | | 精密化 | PDB_EXTRACT | 3.2 | データ抽出 | XDS | | データ削減 | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 5F4O 解像度: 1.81→48.72 Å / SU ML: 0.21 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 18.01
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1829 | 2949 | 5 % |
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Rwork | 0.1526 | - | - |
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obs | 0.1541 | 58952 | 99.49 % |
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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: 100.21 Å2 / Biso mean: 26.3423 Å2 / Biso min: 9.8 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.81→48.72 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4757 | 0 | 90 | 529 | 5376 |
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Biso mean | - | - | 45.11 | 30.95 | - |
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残基数 | - | - | - | - | 611 |
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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_d0.005 | 5059 | X-RAY DIFFRACTION | f_angle_d1.007 | 6921 | X-RAY DIFFRACTION | f_chiral_restr0.04 | 758 | X-RAY DIFFRACTION | f_plane_restr0.005 | 924 | X-RAY DIFFRACTION | f_dihedral_angle_d12.244 | 1836 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | Rms | タイプ |
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1 | 1 | A3500 | X-RAY DIFFRACTION | 5.7 | TORSIONAL1 | 2 | B3500 | X-RAY DIFFRACTION | 5.7 | TORSIONAL | | | |
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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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1.81-1.8397 | 0.3315 | 140 | 0.302 | 2652 | X-RAY DIFFRACTION | 100 | 1.8397-1.8714 | 0.2872 | 138 | 0.2363 | 2632 | X-RAY DIFFRACTION | 100 | 1.8714-1.9054 | 0.2122 | 138 | 0.2102 | 2611 | X-RAY DIFFRACTION | 100 | 1.9054-1.9421 | 0.1987 | 141 | 0.1767 | 2678 | X-RAY DIFFRACTION | 100 | 1.9421-1.9817 | 0.2172 | 139 | 0.1612 | 2646 | X-RAY DIFFRACTION | 100 | 1.9817-2.0248 | 0.2054 | 139 | 0.1558 | 2643 | X-RAY DIFFRACTION | 100 | 2.0248-2.0719 | 0.1974 | 139 | 0.1553 | 2647 | X-RAY DIFFRACTION | 100 | 2.0719-2.1237 | 0.1807 | 139 | 0.1503 | 2628 | X-RAY DIFFRACTION | 99 | 2.1237-2.1812 | 0.2002 | 139 | 0.1485 | 2642 | X-RAY DIFFRACTION | 100 | 2.1812-2.2453 | 0.1815 | 139 | 0.1413 | 2651 | X-RAY DIFFRACTION | 99 | 2.2453-2.3178 | 0.1643 | 139 | 0.1409 | 2630 | X-RAY DIFFRACTION | 99 | 2.3178-2.4007 | 0.1508 | 137 | 0.1409 | 2611 | X-RAY DIFFRACTION | 98 | 2.4007-2.4968 | 0.177 | 134 | 0.1434 | 2543 | X-RAY DIFFRACTION | 96 | 2.4968-2.6104 | 0.1855 | 141 | 0.1509 | 2673 | X-RAY DIFFRACTION | 100 | 2.6104-2.748 | 0.1993 | 141 | 0.153 | 2683 | X-RAY DIFFRACTION | 100 | 2.748-2.9202 | 0.1891 | 141 | 0.1509 | 2678 | X-RAY DIFFRACTION | 100 | 2.9202-3.1456 | 0.178 | 142 | 0.1494 | 2703 | X-RAY DIFFRACTION | 100 | 3.1456-3.4621 | 0.1824 | 142 | 0.1461 | 2697 | X-RAY DIFFRACTION | 100 | 3.4621-3.9628 | 0.18 | 144 | 0.1375 | 2740 | X-RAY DIFFRACTION | 100 | 3.9628-4.992 | 0.1362 | 145 | 0.1233 | 2747 | X-RAY DIFFRACTION | 100 | 4.992-48.72 | 0.1806 | 152 | 0.1696 | 2868 | X-RAY DIFFRACTION | 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 | 2.1858 | -0.2684 | 0.2088 | 1.5659 | 0.4931 | 2.2242 | 0.0421 | -0.0948 | 0.1292 | 0.0135 | -0.082 | -0.0629 | -0.0596 | -0.0486 | 0.0297 | 0.1119 | -0.0342 | 0.0342 | 0.0994 | -0.0304 | 0.1466 | -38.5975 | 12.5769 | 3.5655 | 2 | 2.2355 | 0.5353 | 1.2332 | 1.5673 | 1.172 | 3.5016 | 0.0486 | -0.0042 | -0.0024 | 0.0069 | -0.1196 | 0.2078 | 0.0608 | -0.1939 | 0.0394 | 0.1057 | -0.0035 | 0.0166 | 0.1241 | -0.0231 | 0.1781 | -52.7826 | 1.2502 | -9.8837 | 3 | 1.467 | -0.0468 | -0.5365 | 3.7448 | 0.8795 | 1.5674 | -0.0036 | 0.0506 | -0.0305 | -0.2143 | -0.1075 | 0.0627 | -0.0153 | -0.0983 | 0.1107 | 0.0577 | 0.0122 | -0.0195 | 0.1094 | -0.0097 | 0.0556 | -47.4929 | -2.5114 | -16.1357 | 4 | 1.2927 | -0.1022 | -0.0361 | 2.1994 | 0.8362 | 1.2018 | 0.0571 | 0.102 | 0.1681 | -0.2019 | -0.1128 | 0.0782 | -0.1317 | -0.1434 | 0.0454 | 0.113 | 0.0225 | 0.0004 | 0.1309 | 0.0009 | 0.1175 | -49.7466 | 7.8957 | -16.3996 | 5 | 0.5969 | 0.1428 | -0.2842 | 1.0522 | 0.006 | 2.3751 | 0.0298 | -0.0878 | 0.202 | 0.0829 | -0.1024 | 0.1023 | -0.054 | -0.0356 | 0.0536 | 0.0912 | -0.0227 | 0.0161 | 0.1374 | -0.033 | 0.1931 | -38.4607 | 14.9886 | 0.5695 | 6 | 5.2717 | 0.5642 | -1.8846 | 2.739 | 0.5306 | 3.0685 | 0.0457 | -0.4801 | 0.159 | 0.1824 | 0.0912 | -0.4466 | 0.0847 | 0.1599 | -0.1008 | 0.1889 | -0.022 | -0.0255 | 0.2094 | -0.085 | 0.2096 | -34.2351 | 14.8565 | 16.6791 | 7 | 2.6263 | -0.7993 | 0.4866 | 2.127 | -0.128 | 2.588 | 0.0019 | 0.1098 | 0.0712 | -0.0581 | 0.0298 | -0.4863 | -0.2119 | 0.2049 | -0.0161 | 0.1528 | -0.0619 | 0.0269 | 0.1643 | -0.0877 | 0.2938 | -33.7989 | 21.4914 | 8.1668 | 8 | 3.0845 | -1.0401 | -1.1512 | 5.8653 | 2.1209 | 3.3906 | -0.1032 | -0.3193 | 0.4631 | 0.1684 | 0.1583 | -0.2251 | -0.0667 | -0.018 | -0.0179 | 0.1406 | -0.0325 | -0.036 | 0.2593 | -0.0927 | 0.2249 | -36.4756 | 20.9724 | 17.2474 | 9 | 1.5533 | -0.5718 | -0.144 | 1.5826 | -0.6934 | 2.1275 | 0.1378 | -0.2572 | 0.0842 | 0.1883 | -0.0513 | 0.0377 | -0.1025 | -0.0438 | -0.0507 | 0.17 | -0.058 | 0.0039 | 0.1461 | 0.0011 | 0.1179 | -38.4712 | -8.3228 | 5.3247 | 10 | 3.5878 | 2.7643 | 0.335 | 3.0103 | -0.0935 | 0.7825 | -0.0651 | 0.1851 | -0.2498 | -0.0082 | -0.0341 | -0.3184 | 0.3768 | 0.0942 | 0.0795 | 0.2667 | 0.0135 | 0.0415 | 0.1669 | 0.0458 | 0.1726 | -30.5021 | -19.587 | 0.577 | 11 | 2.2368 | 0.2838 | -1.0672 | 1.7353 | -0.8078 | 2.8472 | 0.0663 | 0.0842 | 0.0769 | -0.0707 | -0.1525 | -0.3261 | 0.0918 | 0.2351 | 0.0595 | 0.117 | 0.0259 | 0.0293 | 0.1494 | 0.0569 | 0.2373 | -20.5132 | -0.8906 | -9.9862 | 12 | 0.9671 | 0.1466 | 0.322 | 1.5505 | -0.1664 | 1.1666 | 0.027 | 0.0634 | 0.0977 | -0.0323 | -0.1295 | -0.0453 | 0.0284 | 0.1472 | 0.1063 | 0.086 | 0.0123 | 0.0545 | 0.1507 | 0.0478 | 0.1355 | -25.8438 | 2.85 | -15.3501 | 13 | 1.2372 | -0.2575 | 0.0989 | 1.6786 | -0.4458 | 1.0224 | 0.0515 | 0.11 | -0.0742 | -0.1683 | -0.173 | -0.2155 | 0.1952 | 0.2064 | 0.1168 | 0.1598 | 0.039 | 0.0631 | 0.1601 | 0.0379 | 0.1523 | -23.4823 | -7.1442 | -16.1871 | 14 | 1.0968 | 0.2454 | 0.3312 | 1.3801 | 0.0631 | 1.7548 | 0.0926 | -0.0945 | -0.1523 | 0.1667 | -0.1353 | -0.1244 | 0.2948 | 0.0512 | 0.0126 | 0.1843 | -0.0253 | 0.0283 | 0.1224 | 0.0283 | 0.1385 | -35.2661 | -14.8927 | -0.1573 | 15 | 2.8709 | -0.2172 | 1.1669 | 2.9421 | -0.5796 | 2.5943 | 0.2211 | -0.4135 | -0.2735 | 0.3855 | -0.0396 | 0.2711 | 0.0218 | -0.1517 | -0.175 | 0.2705 | -0.1017 | 0.0277 | 0.2646 | 0.0613 | 0.1386 | -40.0725 | -15.7015 | 16.1387 | 16 | 2.7631 | -0.4178 | -0.3892 | 2.8009 | -0.7882 | 2.2732 | 0.0679 | 0.0081 | -0.2197 | 0.0625 | -0.0636 | 0.1348 | 0.3752 | -0.1934 | 0.0124 | 0.2696 | -0.1046 | 0.002 | 0.1647 | 0.0249 | 0.1968 | -39.9585 | -21.8246 | 7.3431 | 17 | 2.5572 | -0.9635 | 1.5539 | 5.0521 | -2.5848 | 3.4542 | 0.1081 | -0.301 | -0.3712 | 0.2003 | -0.1565 | 0.0974 | 0.4165 | -0.0075 | 0.0482 | 0.3905 | -0.1253 | 0.0355 | 0.298 | 0.0908 | 0.1927 | -37.7689 | -21.1469 | 16.4113 |
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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 224 through 268 )A224 - 268 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 269 through 319 )A269 - 319 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 320 through 347 )A320 - 347 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 348 through 422 )A348 - 422 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 423 through 464 )A423 - 464 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 465 through 484 )A465 - 484 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 485 through 513 )A485 - 513 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 514 through 530 )A514 - 530 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 223 through 247 )B223 - 247 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 248 through 268 )B248 - 268 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 269 through 319 )B269 - 319 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 320 through 347 )B320 - 347 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 348 through 422 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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