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 | PHENIX | 1.18.2_3874精密化 | PDB_EXTRACT | 3.25 | 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: 2h7i 解像度: 1.8→38.85 Å / SU ML: 0.14 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 17.42 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1766 | 1925 | 1.71 % |
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Rwork | 0.1461 | 110611 | - |
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obs | 0.1466 | 112536 | 98.67 % |
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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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原子変位パラメータ | Biso max: 70.22 Å2 / Biso mean: 21.392 Å2 / Biso min: 7.92 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.8→38.85 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 7780 | 0 | 224 | 1276 | 9280 |
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Biso mean | - | - | 18.5 | 30.74 | - |
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残基数 | - | - | - | - | 1060 |
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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: 14 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.8-1.84 | 0.1866 | 153 | 0.1816 | 7667 | 7820 | 96 | 1.85-1.89 | 0.2229 | 131 | 0.1682 | 7823 | 7954 | 98 | 1.89-1.95 | 0.1888 | 127 | 0.1618 | 7825 | 7952 | 98 | 1.95-2.01 | 0.2181 | 141 | 0.1552 | 7851 | 7992 | 98 | 2.01-2.09 | 0.2103 | 147 | 0.1531 | 7858 | 8005 | 99 | 2.09-2.17 | 0.1891 | 133 | 0.1457 | 7833 | 7966 | 98 | 2.17-2.27 | 0.1638 | 123 | 0.14 | 7953 | 8076 | 99 | 2.27-2.39 | 0.1905 | 144 | 0.1451 | 7839 | 7983 | 99 | 2.39-2.54 | 0.1992 | 153 | 0.1519 | 7899 | 8052 | 99 | 2.54-2.73 | 0.1745 | 139 | 0.1515 | 7966 | 8105 | 99 | 2.73-3.01 | 0.1825 | 99 | 0.1466 | 8011 | 8110 | 99 | 3.01-3.44 | 0.163 | 104 | 0.1447 | 7999 | 8103 | 100 | 3.44-4.34 | 0.1426 | 185 | 0.1289 | 7990 | 8175 | 100 | 4.34-38.85 | 0.1772 | 146 | 0.1432 | 8097 | 8243 | 99 |
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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 | 2.6613 | 0.5358 | 0.347 | 2.9497 | -0.4367 | 1.715 | 0.0451 | 0.241 | -0.0002 | -0.1993 | -0.0914 | 0.0888 | -0.0168 | -0.0929 | 0.0842 | 0.1009 | 0.0274 | -0.0066 | 0.1345 | -0.0506 | 0.0749 | 11.0303 | 3.3471 | -6.0811 | 2 | 2.0584 | 0.6542 | 0.5466 | 3.5404 | -1.1675 | 2.3445 | 0.0468 | 0.1656 | -0.4306 | -0.2356 | -0.0257 | 0.1206 | 0.2076 | -0.3612 | -0.0087 | 0.1294 | -0.0036 | -0.0064 | 0.203 | -0.1021 | 0.1642 | 6.442 | -6.5358 | -6.0822 | 3 | 1.3504 | -0.5479 | 0.6882 | 1.0223 | -0.128 | 2.4966 | 0.0108 | 0.2134 | -0.1606 | -0.1066 | -0.1531 | 0.0175 | 0.227 | 0.0795 | 0.097 | 0.1082 | -0.0147 | -0.0054 | 0.1447 | -0.07 | 0.1805 | 11.3855 | -8.1322 | -3.5049 | 4 | 2.4135 | 0.126 | -1.1179 | 1.3422 | -0.7893 | 6.4047 | -0.0175 | 0.1092 | -0.3139 | -0.0003 | -0.0205 | -0.1262 | 0.3732 | 0.3088 | 0.0878 | 0.1504 | 0.0252 | -0.0001 | 0.1466 | -0.0675 | 0.2378 | 20.2736 | -13.2341 | -1.9588 | 5 | 0.6352 | 0.0417 | 0.1042 | 0.7979 | 0.2671 | 1.3261 | 0.0538 | -0.0179 | -0.0877 | 0.0319 | -0.0658 | 0.0211 | 0.1087 | -0.0279 | 0.0067 | 0.0848 | -0.0086 | -0.0009 | 0.0727 | -0.0164 | 0.1278 | 13.7773 | -1.5365 | 10.9769 | 6 | 0.9881 | 0.4996 | -0.091 | 0.9591 | -0.0924 | 0.8433 | 0.0286 | -0.0313 | -0.1077 | 0.0692 | -0.085 | 0.0284 | 0.0475 | -0.0783 | 0.0558 | 0.0927 | -0.0022 | 0.0009 | 0.0677 | -0.0208 | 0.1043 | 12.4965 | 3.3443 | 12.0046 | 7 | 3.2359 | 2.1367 | -0.7025 | 2.2836 | -0.7598 | 1.7799 | 0.0994 | -0.0358 | 0.1936 | 0.2171 | -0.0956 | 0.6067 | 0.0588 | -0.3438 | -0.0498 | 0.119 | -0.0016 | 0.0297 | 0.1979 | -0.0433 | 0.2632 | -3.6755 | 13.9875 | 10.5756 | 8 | 1.2488 | 0.0346 | 0.4153 | 0.7285 | -0.2962 | 0.7485 | -0.0116 | 0.0861 | 0.0015 | -0.0981 | -0.0186 | 0.0656 | -0.0353 | -0.0454 | 0.0377 | 0.1059 | 0.0264 | 0.0144 | 0.1238 | -0.0113 | 0.1185 | 18.456 | 11.9794 | -0.6443 | 9 | 2.8931 | 0.8697 | 2.0903 | 3.4712 | -1.4582 | 4.2967 | 0.0957 | 0.0743 | 0.148 | 0.1752 | -0.1927 | 0.1965 | -0.1555 | -0.312 | 0.1267 | 0.0644 | -0.0227 | 0.0223 | 0.0655 | -0.007 | 0.0848 | 10.4253 | 17.9111 | 12.8001 | 10 | 2.5593 | 0.3591 | -0.2831 | 2.8669 | 0.1982 | 1.8608 | -0.0009 | 0.2957 | 0.0359 | -0.2267 | -0.0897 | -0.0783 | 0.0094 | 0.092 | 0.1026 | 0.101 | 0.0214 | 0.0096 | 0.1374 | 0.0536 | 0.0921 | 26.3537 | 28.8908 | -6.1032 | 11 | 1.8486 | 0.4595 | -0.6854 | 3.0617 | 0.8437 | 2.159 | 0.0278 | 0.2175 | 0.4337 | -0.1901 | -0.0111 | -0.1646 | -0.1792 | 0.3588 | -0.0033 | 0.1313 | 0.0035 | 0.0102 | 0.2348 | 0.119 | 0.22 | 31.2959 | 38.5209 | -6.2759 | 12 | 1.5788 | -0.9048 | -0.9991 | 1.305 | 0.4421 | 3.693 | -0.057 | 0.2465 | 0.2253 | -0.0944 | -0.106 | 0.0065 | -0.0948 | -0.0294 | 0.1435 | 0.1145 | -0.0213 | -0.0018 | 0.1503 | 0.0849 | 0.2115 | 26.0282 | 40.3475 | -3.4718 | 13 | 2.8845 | 0.8314 | 1.9334 | 1.3839 | 1.8552 | 2.996 | -0.0696 | 0.0892 | 0.4535 | -0.0647 | -0.0635 | 0.1147 | -0.4462 | -0.2349 | 0.2123 | 0.1674 | 0.0297 | -0.0196 | 0.1367 | 0.0832 | 0.3049 | 17.1144 | 45.4293 | -1.8262 | 14 | 0.629 | -0.033 | 0.0748 | 0.4591 | -0.0791 | 1.1909 | 0.0066 | 0.0237 | 0.1217 | 0.0076 | -0.0524 | -0.0144 | -0.1165 | 0.0102 | 0.0602 | 0.0923 | -0.0041 | 0.0002 | 0.079 | 0.0197 | 0.1543 | 23.9054 | 33.642 | 11.0599 | 15 | 0.6939 | 0.2217 | 0.2422 | 0.7897 | 0.1016 | 0.7979 | -0.0153 | 0.0242 | 0.1054 | 0.0399 | -0.0477 | -0.0635 | -0.0705 | 0.0734 | 0.0612 | 0.0857 | 0.001 | 0.0027 | 0.0633 | 0.0178 | 0.1077 | 26.4514 | 28.6872 | 12.0923 | 16 | 3.6219 | 2.3826 | 1.0219 | 3.2486 | 0.5789 | 1.4085 | 0.0593 | 0.006 | -0.0899 | 0.2175 | -0.0733 | -0.4113 | 0.0091 | 0.2099 | -0.0054 | 0.1167 | 0.0165 | -0.0085 | 0.1744 | 0.029 | 0.2219 | 40.1922 | 17.3636 | 10.2417 | 17 | 0.9951 | 0.5975 | -0.2214 | 1.2964 | -0.0766 | 1.6013 | 0.0307 | 0.0787 | 0.0536 | -0.0249 | -0.0711 | -0.0273 | 0.0195 | 0.0397 | 0.0513 | 0.085 | 0.0128 | 0.0076 | 0.0848 | 0.0001 | 0.0953 | 22.1465 | 17.7559 | 4.7392 | 18 | 2.9977 | -0.2007 | 0.0465 | 2.5813 | 0.3278 | 1.3342 | 0.0362 | -0.3874 | 0.0511 | 0.4348 | -0.1094 | 0.1206 | -0.0169 | -0.1879 | 0.0555 | 0.2445 | -0.0385 | 0.0193 | 0.2397 | -0.0798 | 0.1151 | 16.1331 | 30.5467 | 48.5037 | 19 | 1.0821 | 0.4789 | -0.9286 | 1.302 | -0.746 | 3.1007 | 0.0525 | -0.2789 | 0.2932 | 0.3451 | -0.0656 | 0.1213 | -0.4078 | -0.2101 | 0.0086 | 0.2869 | 0.0058 | -0.0068 | 0.2746 | -0.1311 | 0.2028 | 17.33 | 41.1423 | 47.401 | 20 | 2.8822 | -1.0696 | 1.2689 | 3.958 | -3.2456 | 2.7696 | -0.0051 | -0.1551 | 0.3218 | 0.3759 | -0.1438 | -0.1638 | -0.5953 | 0.4261 | 0.1796 | 0.2942 | -0.0569 | -0.06 | 0.222 | -0.1107 | 0.2737 | 30.3333 | 43.0076 | 44.1645 | 21 | 0.327 | 0.0426 | -0.1275 | 0.7875 | -0.0695 | 1.7961 | 0.0192 | -0.2153 | 0.1171 | 0.1535 | -0.092 | -0.1463 | -0.0736 | 0.1184 | 0.1031 | 0.1966 | -0.0324 | -0.0231 | 0.167 | -0.0526 | 0.1769 | 24.1667 | 34.8765 | 41.4766 | 22 | 0.9404 | 0.0281 | 0.6325 | 0.8148 | -0.4145 | 1.9897 | -0.0153 | -0.0857 | 0.1793 | 0.1238 | -0.042 | 0.1074 | -0.2198 | -0.1238 | 0.0712 | 0.1531 | 0.0013 | 0.0019 | 0.1165 | -0.0498 | 0.1921 | 19.227 | 38.8706 | 26.4629 | 23 | 0.6186 | 0.3037 | 0.7409 | 0.7862 | 0.2305 | 2.6374 | 0.0314 | -0.1102 | 0.1178 | 0.1295 | -0.0905 | 0.0095 | 0.0943 | -0.0326 | 0.0064 | 0.1623 | -0.0189 | 0.0097 | 0.1446 | -0.0331 | 0.1311 | 18.0295 | 26.5523 | 31.7695 | 24 | 1.3822 | -0.4274 | 0.2946 | 1.2673 | -0.3825 | 1.561 | -0.0455 | -0.1516 | 0.166 | 0.0643 | -0.024 | -0.0525 | -0.0179 | -0.0128 | 0.0783 | 0.1369 | -0.0239 | -0.0025 | 0.0971 | -0.025 | 0.1196 | 24.1053 | 28.8518 | 27.4064 | 25 | 1.8064 | 0.9992 | -0.7046 | 1.3158 | 0.3477 | 1.0665 | -0.163 | 0.092 | 0.4557 | 0.1935 | -0.043 | 0.2102 | -0.2372 | -0.281 | 0.1722 | 0.1973 | 0.0066 | -0.0018 | 0.201 | -0.0488 | 0.1739 | 12.4582 | 29.606 | 34.5376 | 26 | 2.1356 | 0.9535 | -0.1141 | 5.7724 | -0.0238 | 4.9332 | -0.0838 | -0.1034 | 0.3796 | -0.2736 | -0.0787 | 0.9124 | -0.243 | -0.7952 | 0.1591 | 0.1831 | 0.0283 | 0.0102 | 0.326 | -0.0831 | 0.3005 | 0.4573 | 22.9566 | 33.6877 | 27 | 1.6352 | -0.1947 | 0.01 | 1.6512 | -0.0871 | 0.8541 | -0.0143 | -0.1776 | 0.0273 | 0.139 | -0.0607 | 0.1098 | 0.0207 | -0.0965 | 0.076 | 0.1622 | -0.0388 | 0.0228 | 0.1426 | -0.0192 | 0.0866 | 16.2923 | 18.6601 | 37.6615 | 28 | 1.8755 | 0.4393 | -0.7699 | 1.7854 | -0.2655 | 1.4228 | 0.1538 | -0.3096 | -0.0687 | 0.4706 | -0.1168 | -0.1399 | 0.2094 | -0.0938 | 0.011 | 0.3388 | -0.0763 | -0.0158 | 0.2551 | 0.0606 | 0.1047 | 22.0338 | 1.2163 | 48.3085 | 29 | 1.1752 | 0.9456 | 1.0827 | 1.5045 | -0.2127 | 2.5656 | 0.1417 | -0.2342 | -0.3499 | 0.4308 | -0.0779 | -0.1658 | 0.7026 | 0.0805 | -0.0925 | 0.4925 | -0.0445 | -0.0295 | 0.2873 | 0.1221 | 0.2061 | 23.0799 | -9.3633 | 48.1818 | 30 | 0.4081 | -0.136 | 0.0559 | 0.1981 | -0.4483 | 1.2013 | 0.0638 | -0.2078 | -0.1912 | 0.3649 | -0.1087 | -0.0035 | 0.3867 | -0.1466 | -0.1537 | 0.4473 | -0.1083 | 0.0008 | 0.2316 | 0.0856 | 0.1636 | 17.8432 | -9.4441 | 45.6932 | 31 | 2.3232 | -0.3448 | -0.7574 | 1.5048 | 0.3613 | 5.966 | -0.0501 | -0.0703 | -0.2204 | 0.3483 | -0.1376 | 0.2405 | 0.5372 | -0.5657 | 0.1336 | 0.4334 | -0.1703 | 0.0643 | 0.3244 | 0.0606 | 0.2621 | 7.7884 | -11.2076 | 44.22 | 32 | 2.3377 | -1.1783 | -1.8425 | 1.0624 | 0.7446 | 4.256 | -0.0874 | -0.3662 | -0.3079 | 0.2446 | -0.0403 | 0.2086 | 0.3188 | -0.1002 | 0.2655 | 0.2417 | -0.101 | 0.0287 | 0.2153 | 0.0471 | 0.1646 | 14.3607 | -2.8655 | 41.1257 | 33 | 4.86 | 1.5602 | 0.3183 | 4.0373 | -2.1054 | 3.4855 | 0.0704 | -0.2465 | -0.0108 | 0.0791 | -0.0801 | -0.413 | 0.1429 | 0.395 | -0.0105 | 0.1739 | 0.0349 | -0.0054 | 0.1671 | -0.0167 | 0.2614 | 29.3968 | -8.376 | 17.6642 | 34 | 1.1215 | -0.0164 | 0.131 | 1.1482 | 0.1318 | 1.4197 | 0.0803 | -0.1966 | -0.0955 | 0.1909 | -0.106 | 0.0427 | 0.1117 | -0.1636 | 0.02 | 0.1454 | -0.0543 | 0.008 | 0.128 | 0.0204 | 0.0997 | 15.3252 | 0.7274 | 29.9918 | 35 | 0.7315 | -0.3612 | 0.1663 | 0.8059 | -0.1176 | 0.384 | -0.0488 | 0.2018 | -0.3132 | 0.1449 | -0.0994 | -0.0379 | 0.2945 | 0.0608 | 0.1589 | 0.2403 | -0.0054 | 0.0097 | 0.1882 | 0.0238 | 0.1766 | 27.5058 | 0.8615 | 33.6384 | 36 | 1.7739 | -2.0327 | 0.3152 | 6.3196 | -0.0457 | 0.6027 | 0.0443 | 0.0152 | -0.275 | -0.2661 | -0.1162 | -0.9745 | 0.3107 | 0.2139 | -0.0408 | 0.233 | -0.0095 | 0.0137 | 0.2018 | 0.0185 | 0.2725 | 38.1257 | 8.5123 | 32.3728 | 37 | 1.4524 | -0.3775 | 0.4123 | 1.8093 | 0.2533 | 0.9429 | 0.0469 | -0.2217 | -0.0204 | 0.2123 | -0.0666 | -0.0207 | 0.0831 | -0.0567 | 0.0186 | 0.1534 | -0.0452 | -0.0107 | 0.1245 | -0.0008 | 0.073 | 21.6227 | 13.2523 | 37.5932 |
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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 through 31 )A2 - 31 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 32 through 53 )A32 - 53 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 54 through 67 )A54 - 67 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 68 through 82 )A68 - 82 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 83 through 158 )A83 - 158 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 159 through 207 )A159 - 207 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 208 through 235 )A208 - 235 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 236 through 255 )A236 - 255 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 256 through 269 )A256 - 269 | 10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 2 through 31 )C2 - 31 | 11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 32 through 53 )C32 - 53 | 12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 54 through 67 )C54 - 67 | 13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 68 through 82 )C | | | | | | | | | | | | | | | | | | | | | | | | | |
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