ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.13_2998: ???)精密化 | XDS | | データ削減 | Aimless | | データスケーリング | PHASER | | 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: 1.703→46.597 Å / SU ML: 0.15 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 20.16 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.1822 | 1994 | 2.13 % | 5 |
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Rwork | 0.1599 | - | - | - |
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obs | 0.1603 | 93415 | 93.49 % | - |
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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 / 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: 1.703→46.597 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6160 | 0 | 0 | 750 | 6910 |
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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_d0.012 | 6320 | X-RAY DIFFRACTION | f_angle_d1.102 | 8562 | X-RAY DIFFRACTION | f_dihedral_angle_d11.832 | 3710 | X-RAY DIFFRACTION | f_chiral_restr0.084 | 909 | X-RAY DIFFRACTION | f_plane_restr0.007 | 1093 | | | | | |
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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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1.7031-1.7457 | 0.2609 | 86 | 0.2466 | 4007 | X-RAY DIFFRACTION | 57 | 1.7457-1.7929 | 0.2728 | 154 | 0.221 | 6626 | X-RAY DIFFRACTION | 96 | 1.7929-1.8457 | 0.2041 | 148 | 0.2014 | 6959 | X-RAY DIFFRACTION | 100 | 1.8457-1.9052 | 0.2369 | 122 | 0.1905 | 6029 | X-RAY DIFFRACTION | 86 | 1.9052-1.9733 | 0.1891 | 136 | 0.1678 | 5749 | X-RAY DIFFRACTION | 83 | 1.9733-2.0524 | 0.2108 | 140 | 0.158 | 6115 | X-RAY DIFFRACTION | 88 | 2.0524-2.1458 | 0.1973 | 149 | 0.1574 | 6962 | X-RAY DIFFRACTION | 100 | 2.1458-2.2589 | 0.2086 | 149 | 0.1589 | 6969 | X-RAY DIFFRACTION | 100 | 2.2589-2.4004 | 0.1647 | 157 | 0.165 | 6965 | X-RAY DIFFRACTION | 100 | 2.4004-2.5857 | 0.1775 | 150 | 0.1744 | 6967 | X-RAY DIFFRACTION | 100 | 2.5857-2.8459 | 0.1959 | 150 | 0.1672 | 6959 | X-RAY DIFFRACTION | 100 | 2.8459-3.2576 | 0.2086 | 150 | 0.1632 | 7000 | X-RAY DIFFRACTION | 100 | 3.2576-4.1039 | 0.1357 | 150 | 0.1396 | 7004 | X-RAY DIFFRACTION | 100 | 4.1039-46.6143 | 0.1655 | 153 | 0.1437 | 7110 | 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 | 1.2694 | -0.1146 | 0.4261 | 2.1524 | -0.0539 | 2.0776 | 0.1162 | 0.1712 | -0.0436 | -0.1514 | 0.0472 | -0.4638 | 0.0767 | 0.5725 | -0.1756 | 0.1696 | 0.0307 | 0.0326 | 0.2689 | -0.0555 | 0.2491 | 8.1673 | 7.0183 | -1.7771 | 2 | 2.9358 | 0.9974 | 1.6032 | 3.1717 | 1.5331 | 3.0077 | 0.1597 | -0.3897 | 0.0518 | 0.3751 | -0.1116 | 0.0163 | 0.0379 | -0.0887 | -0.0416 | 0.2092 | -0.0326 | 0.0094 | 0.1994 | -0.0117 | 0.1262 | -1.7811 | 12.2401 | 13.9837 | 3 | 2.6042 | 0.2678 | -0.0909 | 3.5888 | 0.7248 | 4.7887 | -0.0406 | 0.194 | -0.0105 | -0.3617 | -0.0322 | -0.1407 | -0.0518 | 0.296 | 0.0078 | 0.1798 | 0.0121 | 0.0079 | 0.1725 | -0.0133 | 0.1594 | -4.7597 | 9.2792 | -5.3502 | 4 | 2.1567 | 0.1575 | -0.1601 | 2.9283 | -0.1304 | 2.2918 | 0.1698 | -0.1873 | 0.2507 | 0.0997 | -0.1048 | -0.216 | -0.2778 | 0.1258 | -0.0991 | 0.2344 | -0.0197 | 0.0168 | 0.1924 | -0.0241 | 0.2059 | -0.7241 | 20.1052 | 8.1296 | 5 | 3.4895 | -0.648 | 0.759 | 2.9353 | 1.0111 | 3.7717 | 0.0397 | -0.0996 | 0.0945 | 0.1981 | -0.0845 | -0.1 | 0.0869 | 0.2481 | -0.0489 | 0.1483 | -0.0316 | 0.0085 | 0.1697 | -0.036 | 0.1528 | 2.6803 | 14.0964 | 8.677 | 6 | 1.4 | 0.0739 | 0.7922 | 2.1606 | 0.3388 | 1.613 | 0.0884 | 0.1288 | 0.0505 | -0.2891 | -0.0703 | 0.0652 | -0.0387 | 0.0156 | -0.014 | 0.2003 | 0.024 | 0.0112 | 0.1704 | -0.0096 | 0.158 | -8.1606 | 8.977 | -5.0576 | 7 | 3.4448 | 0.9829 | 0.1269 | 3.7986 | -1.3768 | 1.2687 | 0.2042 | -0.1747 | 0.1023 | -0.0555 | -0.2457 | 0.402 | -0.2031 | -0.8388 | -0.0654 | 0.225 | 0.126 | -0.0701 | 0.3435 | -0.0582 | 0.2639 | -26.1616 | 13.6928 | -7.5376 | 8 | 1.9375 | 1.7069 | 1.7538 | 6.644 | 4.9045 | 7.0888 | 0.0687 | 0.9344 | 0.1145 | -0.4541 | -0.7134 | 1.6683 | 0.1561 | -1.1509 | 0.0568 | 0.3736 | 0.0848 | -0.1422 | 0.6483 | -0.0449 | 0.7104 | -33.3116 | 8.6142 | -13.674 | 9 | 1.4445 | 0.8649 | 1.0875 | 0.9516 | 0.0825 | 2.2896 | 0.0824 | 0.4174 | -0.0301 | -0.3878 | -0.1144 | 0.2933 | -0.0694 | -0.3232 | 0.0659 | 0.2879 | 0.0852 | -0.1051 | 0.3126 | -0.077 | 0.2382 | -18.3012 | 6.4983 | -14.9992 | 10 | 1.36 | -0.0314 | 1.6565 | 0.951 | 0.37 | 2.9311 | 0.1643 | 0.1134 | -0.0031 | -0.3131 | -0.1045 | 0.333 | -0.1504 | -0.1824 | -0.0799 | 0.211 | 0.0497 | -0.0589 | 0.2169 | -0.0489 | 0.2237 | -18.1023 | 7.2842 | -6.8635 | 11 | 2.646 | 0.9527 | 1.3713 | 3.5861 | 0.4169 | 3.2746 | 0.3077 | -0.5021 | 0.4222 | 0.3996 | -0.1429 | 0.5661 | 0.2174 | -0.7125 | -0.2018 | 0.2078 | -0.0736 | 0.06 | 0.3428 | -0.0064 | 0.3646 | -22.6684 | -14.6058 | -43.246 | 12 | 3.8076 | -0.4146 | 1.9843 | 4.0303 | -1.6096 | 3.3073 | 0.0226 | 0.6512 | 0.2143 | -0.4094 | -0.0588 | 0.3678 | -0.0088 | 0.0403 | 0.0248 | 0.2718 | 0.0528 | -0.0368 | 0.2886 | 0.0245 | 0.1951 | -13.7576 | -10.5792 | -60.1045 | 13 | 2.9091 | 0.5717 | 0.542 | 3.8107 | -1.0029 | 5.0775 | 0.1194 | -0.1815 | 0.155 | 0.2453 | -0.107 | 0.1478 | -0.192 | -0.3061 | 0.0078 | 0.1294 | 0.0057 | 0.0183 | 0.1447 | -0.0167 | 0.165 | -10.1176 | -12.484 | -40.5796 | 14 | 2.6492 | -0.0779 | 0.1347 | 4.8611 | -0.2596 | 2.9179 | 0.1447 | 0.1849 | 0.5562 | -0.2944 | -0.1145 | 0.5676 | -0.3368 | -0.1333 | 0.0373 | 0.2485 | 0.0456 | -0.0007 | 0.216 | 0.0198 | 0.3387 | -14.4155 | -2.2527 | -54.6447 | 15 | 4.0895 | 1.4828 | 0.2564 | 3.8229 | -0.3293 | 3.2156 | 0.0165 | 0.3547 | 0.1724 | -0.3991 | -0.0461 | 0.5191 | 0.1084 | -0.3092 | 0.0104 | 0.1797 | 0.0599 | -0.0491 | 0.226 | 0.0344 | 0.2759 | -17.8997 | -8.1346 | -54.7113 | 16 | 1.1849 | -0.0478 | 1.162 | 1.8899 | -0.1728 | 2.0274 | 0.05 | -0.1032 | 0.0479 | 0.0887 | -0.0789 | 0.1098 | 0.1715 | -0.0813 | -0.028 | 0.1379 | 0.0129 | 0.0402 | 0.1826 | -0.0027 | 0.1593 | -9.5069 | -14.8123 | -42.5053 | 17 | 3.3975 | -0.1631 | 0.6218 | 3.1163 | -0.3744 | 2.5227 | 0.0125 | 0.1592 | 0.3569 | 0.0445 | -0.0708 | -0.2537 | -0.2687 | 0.2955 | 0.0259 | 0.1649 | -0.0512 | 0.0156 | 0.1722 | 0.0182 | 0.1726 | 7.2598 | -8.2833 | -38.5936 | 18 | 3.457 | -0.1844 | 0.0471 | 6.5073 | -2.3207 | 5.7112 | -0.2389 | -0.2397 | -0.0997 | 0.5351 | -0.2988 | -1.657 | -0.1834 | 1.2371 | -0.1116 | 0.2039 | -0.0317 | -0.0127 | 0.4658 | -0.0296 | 0.5534 | 18.5782 | -13.4996 | -33.168 | 19 | 1.558 | -0.3468 | 0.3288 | 1.3192 | -0.1167 | 2.647 | -0.0194 | -0.1744 | 0.0689 | 0.1848 | -0.1045 | -0.1715 | 0.0424 | 0.1499 | 0.0272 | 0.1678 | -0.0254 | -0.0036 | 0.1728 | 0.0028 | 0.1478 | 3.4265 | -14.8167 | -30.4164 | 20 | 1.416 | -0.5008 | 1.2983 | 1.0766 | -0.2852 | 2.5577 | 0.0752 | 0.0416 | 0.0716 | 0.0439 | -0.0525 | -0.0456 | -0.0837 | 0.0967 | -0.0207 | 0.1535 | -0.0129 | 0.0178 | 0.1663 | 0.0068 | 0.1744 | 3.0868 | -14.4672 | -39.4368 | 21 | 3.6708 | -0.8365 | -1.4605 | 3.195 | 0.7294 | 2.5708 | 0.2952 | 0.6528 | -0.417 | -0.2668 | -0.243 | 0.479 | -0.1663 | -0.6409 | -0.0461 | 0.3106 | 0.0891 | -0.0523 | 0.4465 | -0.0506 | 0.5548 | -35.6335 | -7.6117 | -2.3128 | 22 | 3.7394 | 0.2639 | -1.21 | 3.4637 | -0.4554 | 3.5838 | -0.0753 | -0.8967 | -0.3286 | 0.4434 | 0.013 | 0.4393 | 0.1001 | -0.2958 | -0.0409 | 0.2978 | -0.0734 | 0.0804 | 0.41 | 0.002 | 0.3318 | -26.7721 | -11.2008 | 14.6482 | 23 | 3.7467 | -0.4695 | 1.185 | 3.5875 | -0.7373 | 7.264 | 0.0443 | 0.1588 | -0.1367 | -0.2015 | -0.1857 | 0.3677 | 0.2769 | -0.4953 | 0.0424 | 0.1775 | -0.0251 | -0.0044 | 0.2465 | -0.0857 | 0.2798 | -23.1162 | -9.5418 | -4.8022 | 24 | 5.2447 | -0.4136 | 0.1879 | 3.6629 | -0.6549 | 2.6517 | 0.1341 | -0.5292 | -0.4268 | 0.3873 | 0.002 | 0.4304 | 0.1256 | -0.3809 | -0.0255 | 0.2826 | -0.0591 | 0.028 | 0.3276 | 0.0334 | 0.3967 | -29.3851 | -16.2412 | 9.3287 | 25 | 2.5616 | -0.2069 | -0.7607 | 2.5292 | -0.3589 | 2.2968 | 0.146 | 0.1088 | -0.0881 | -0.0664 | -0.2004 | 0.3439 | -0.0153 | -0.0157 | -0.0675 | 0.1893 | 0.0049 | -0.0407 | 0.2332 | -0.0591 | 0.2911 | -22.4559 | -7.3217 | -3.0032 | 26 | 3.6346 | -0.328 | -0.6238 | 2.3892 | 0.2197 | 3.5332 | 0.017 | 0.1501 | -0.1732 | -0.0515 | -0.0565 | -0.165 | -0.0002 | 0.2379 | 0.0668 | 0.1822 | 0.0177 | -0.0201 | 0.1703 | -0.0428 | 0.1642 | -3.2979 | -10.5984 | -10.649 | 27 | 1.1943 | -0.0154 | -1.1015 | 1.053 | 0.3684 | 2.8713 | 0.1036 | 0.0532 | -0.0802 | -0.0952 | -0.0577 | 0.0919 | 0.1003 | -0.0406 | -0.0378 | 0.2009 | 0.0085 | -0.0042 | 0.1915 | -0.0286 | 0.1776 | -9.738 | -7.6811 | -5.9382 | 28 | 2.2867 | 0.2161 | -0.4146 | 3.069 | -0.2828 | 2.6711 | 0.1838 | -0.0733 | -0.138 | 0.178 | -0.0828 | -0.8237 | -0.1721 | 0.6508 | -0.1201 | 0.1724 | -0.0421 | -0.018 | 0.2697 | -0.0134 | 0.4217 | 20.4038 | -29.1943 | -43.2225 | 29 | 3.2613 | -0.8137 | -0.6185 | 3.1843 | 0.7882 | 2.6461 | 0.2023 | 0.7287 | -0.0055 | -0.6202 | -0.1378 | -0.3575 | -0.0545 | 0.1235 | -0.0303 | 0.3006 | 0.0598 | 0.0746 | 0.2997 | -0.032 | 0.2292 | 11.2869 | -34.1113 | -59.6853 | 30 | 3.4324 | -0.291 | 1.4696 | 3.2038 | 0.8378 | 6.5626 | -0.098 | -0.1578 | -0.1216 | 0.1421 | 0.0598 | -0.2797 | -0.0183 | 0.316 | -0.0204 | 0.1334 | 0.0162 | -0.0064 | 0.1587 | 0.0054 | 0.1894 | 7.9639 | -31.4492 | -40.4308 | 31 | 3.3313 | -0.1533 | 0.3364 | 2.6603 | 0.9898 | 2.6684 | 0.2013 | 0.3824 | -0.1304 | -0.4319 | -0.086 | -0.4785 | 0.091 | 0.2675 | -0.1176 | 0.2201 | 0.0602 | 0.0722 | 0.2314 | -0.043 | 0.2866 | 14.1122 | -38.6854 | -54.1149 | 32 | 1.6513 | -0.2691 | -0.2394 | 2.0679 | 0.1766 | 1.877 | 0.0095 | -0.0526 | -0.0137 | -0.0473 | -0.0746 | -0.1924 | -0.041 | -0.0115 | 0.0141 | 0.1227 | 0.0033 | 0.0026 | 0.1508 | -0.0008 | 0.1801 | 7.3638 | -29.241 | -42.305 | 33 | 4.3917 | -0.654 | -1.2166 | 2.3767 | -0.1029 | 1.6484 | 0.055 | 0.1617 | -0.2696 | 0.0842 | -0.12 | 0.2177 | 0.1005 | -0.302 | 0.0337 | 0.1476 | -0.0304 | -0.0053 | 0.1642 | -0.0098 | 0.1889 | -9.4207 | -35.8789 | -37.7232 | 34 | 4.4582 | 1.6983 | 1.7059 | 6.4755 | 5.3015 | 6.5127 | -0.2153 | -0.6603 | 0.4145 | 0.2895 | -0.9158 | 2.1982 | -0.2132 | -1.0667 | 0.0949 | 0.279 | -0.008 | 0.0346 | 0.3937 | -0.0483 | 0.6404 | -20.7279 | -30.9289 | -32.2384 | 35 | 1.9269 | 0.7678 | 0.594 | 3.0185 | 0.9528 | 1.6846 | 0.0936 | -0.308 | -0.0034 | 0.5104 | -0.2272 | 0.2107 | 0.0554 | -0.0995 | 0.0691 | 0.1832 | -0.0377 | 0.0214 | 0.1547 | -0.0062 | 0.1433 | -5.6072 | -28.5279 | -30.1558 | 36 | 1.0926 | 0.1951 | -1.2962 | 1.4 | 0.5145 | 3.2708 | 0.1272 | 0.0036 | -0.1018 | 0.1411 | -0.0948 | 0.0957 | 0.0828 | -0.1346 | -0.0564 | 0.161 | -0.0026 | -0.0086 | 0.1708 | -0.0011 | 0.1589 | -5.3532 | -29.5487 | -39.0777 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 1 through 29 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 30 through 49 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 50 through 66 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 67 through 79 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 80 through 98 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 99 through 124 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 125 through 137 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 138 through 150 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 151 through 164 )10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 165 through 194 )11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 2 through 29 )12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 30 through 49 )13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 50 through 66 )14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 67 through 79 )15 | X-RAY DIFFRACTION | 15 | chain 'C' and (resid 80 through 98 )16 | X-RAY DIFFRACTION | 16 | chain 'C' | | | | | | | | | | | | | | | |
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