ソフトウェア 名称 バージョン 分類 NB XSCALEデータスケーリング Show PHASER位相決定 Show REFMAC5.6.0117精密化 Show PDB_EXTRACT3.11 データ抽出 Show StructureStudioデータ収集 XDSデータ削減
精密化 構造決定の手法 : 分子置換開始モデル : 2KAU解像度 : 2.1→50 Å / Cor.coef. Fo :Fc : 0.96 / Cor.coef. Fo :Fc free : 0.939 / Occupancy max : 1 / Occupancy min : 0.5 / SU B : 6.491 / SU ML : 0.088 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.031 / ESU R Free : 0.028 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLYRfactor 反射数 %反射 Selection details Rfree 0.1878 2374 4.9 % RANDOM Rwork 0.1509 - - - all 0.1527 48876 - - obs 0.1527 48192 97.88 % -
溶媒の処理 イオンプローブ半径 : 0.8 Å / 減衰半径 : 0.8 Å / VDWプローブ半径 : 1.2 Å / 溶媒モデル : MASK原子変位パラメータ Biso max : 61.95 Å2 / Biso mean : 30.876 Å2 / Biso min : 3.75 Å2 Baniso -1 Baniso -2 Baniso -3 1- -16 Å2 -0 Å2 -0 Å2 2- - -19.81 Å2 -0 Å2 3- - - 35.81 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.1→50 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4493 0 17 382 4892
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.011 0.019 4778 X-RAY DIFFRACTION r_angle_refined_deg1.444 2.002 6526 X-RAY DIFFRACTION r_dihedral_angle_1_deg4.683 5 652 X-RAY DIFFRACTION r_dihedral_angle_2_deg29.642 25.179 195 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.854 15 876 X-RAY DIFFRACTION r_dihedral_angle_4_deg14.959 15 27 X-RAY DIFFRACTION r_chiral_restr0.083 0.2 792 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.021 3551
LS精密化 シェル 解像度 : 2.1→2.149 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.226 152 - Rwork 0.171 2779 - all - 2931 - obs - - 81.39 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 42) 大きな表を隠す 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)1 10.4659 -0.6907 0.6773 6.6965 -1.5736 9.4982 -0.3534 -1.0575 -0.193 1.1124 0.3434 0.4216 -0.1773 -0.5048 0.01 0.3826 0.023 0.0391 0.3353 0.0203 0.2106 -4.053 63.9174 23.5253 2 6.556 1.1623 -1.2624 3.2649 -0.1915 1.327 0.0146 0.3924 0.1052 -0.2881 0.1708 0.1072 -0.0399 0.0104 -0.1854 0.0966 0.0097 -0.012 0.1259 -0.0396 0.104 9.9645 63.8772 11 3 4.7827 -2.9925 -1.5497 3.6516 -0.0911 1.1472 0.1972 0.3434 -0.5143 -0.324 -0.3633 0.2202 0.0233 0.0076 0.1661 0.18 -0.0043 -0.0121 0.2264 -0.1411 0.4135 -2.2007 52.541 10.1858 4 10.4964 -0.0366 -8.5429 2.7212 1.2686 28.2047 -0.5142 0.2342 -0.6865 -0.1309 -0.1166 0.4665 0.8796 -0.0011 0.6308 0.0953 0.0069 -0.0558 0.0358 -0.1139 0.421 2.4277 45.3086 8.5124 5 4.6892 -0.0847 2.3772 6.5 0.7041 6.1664 0.0611 0.3855 -0.2197 -0.5442 -0.1245 -0.0836 0.2115 0.1638 0.0635 0.081 0.0188 0.0398 0.1306 -0.111 0.1518 17.704 54.3284 8.6351 6 13.766 0.1234 -0.5412 1.0895 0.5484 0.3049 -0.0759 -0.0487 -0.1403 0.2805 0.0103 0.1471 0.1542 0.0031 0.0656 0.1046 0.0018 0.0032 0.187 0.0273 0.2954 2.0847 50.0229 18.3642 7 10.5162 1.4022 -5.2168 6.4821 -0.8767 4.6735 0.192 0.1281 -0.8312 -0.1446 0.0723 0.3639 0.3216 -0.182 -0.2642 0.134 -0.0114 -0.1284 0.1336 -0.0204 0.3625 9.0342 47.613 14.6001 8 6.9185 -2.8697 3.7573 7.4696 -7.1623 22.3694 0.0967 -1.0536 -0.6125 0.2291 0.3167 0.0355 1.2628 -0.1791 -0.4134 0.3048 -0.0086 -0.0701 0.2639 0.063 0.2127 9.9642 70.2392 22.6536 9 8.0266 -2.2704 3.2444 4.9871 -3.1009 6.8848 0.387 0.0139 -0.541 -0.3421 0.0314 0.0719 0.437 -0.0142 -0.4184 0.1171 -0.0023 -0.0441 0.0799 -0.0147 0.1189 3.8196 77.596 11.1991 10 3.9814 -1.9471 0.9363 2.8495 -0.3719 0.3626 0.0891 0.2256 0.0379 -0.1493 -0.0463 -0.1204 -0.0588 0.0278 -0.0428 0.1312 -0.011 -0.0067 0.118 0.0196 0.0744 6.0313 83.9802 10.181 11 0.5472 -1.2713 -0.0062 19.6519 -4.1528 1.0796 0.1466 -0.0464 0.1155 -0.5107 -0.211 -0.3876 0.0142 0.1526 0.0644 0.1106 -0.0247 0.0456 0.1943 0.013 0.2375 22.2905 81.4047 8.7521 12 3.7987 0.3961 -1.1505 4.6107 1.0317 6.0308 -0.1177 0.3041 0.2689 -0.3013 0.0845 0.0282 -0.2792 0.0542 0.0332 0.1132 -0.0253 0.0002 0.1001 0.0501 0.0866 6.2643 93.8978 8.9482 13 4.0291 -6.3145 0.2606 12.1033 -0.2987 1.1637 -0.0058 -0.2208 -0.0365 0.0261 -0.0722 -0.4043 0.0189 0.2364 0.078 0.1386 0.015 -0.0406 0.1915 0.0449 0.2407 19.9806 81.538 18.1351 14 2.6701 1.3712 -0.7353 5.4718 -0.0498 2.0483 -0.0142 0.199 0.2233 0.1982 0.0181 -0.6545 -0.0397 0.4052 -0.0038 0.1587 -0.033 -0.0083 0.1867 0.0121 0.1934 18.0502 89.2816 14.5723 15 0.6374 -1.3621 0.0464 4.3999 2.7272 7.1777 -0.1237 -0.1112 0.3429 0.5882 0.0839 -0.7069 -0.0779 0.6271 0.0399 0.5149 -0.1779 -0.0465 0.6729 -0.0512 0.3601 -1.6123 79.4638 23.5842 16 0.8601 0.6113 -0.312 6.251 1.6826 1.9832 -0.0276 0.069 0.0081 -0.1554 0.1274 -0.1907 -0.0498 0.0933 -0.0998 0.0724 -0.0144 0.0012 0.1539 -0.0121 0.0655 -9.4023 67.981 10.9176 17 3.9454 -1.5566 -0.6382 1.7055 0.9022 0.5116 -0.1955 0.6152 -0.1665 -0.2549 0.0443 0.3235 -0.1168 0.0864 0.1512 0.2607 -0.0401 -0.0801 0.2647 0.057 0.2692 -12.2015 84.8935 10.6281 18 8.4182 -0.1515 -1.0492 9.2256 -5.6324 20.6057 -0.1278 0.2321 0.1781 0.1735 -0.1945 0.6967 -0.4793 -0.8795 0.3223 0.0811 0.0008 -0.0534 0.1504 0.0279 0.2195 -21.6614 82.9595 8.9111 19 3.8573 0.4455 -1.0069 8.1002 -1.573 6.6386 -0.0493 0.4327 -0.1562 -0.6102 -0.0262 0.2299 -0.0397 -0.237 0.0755 0.0957 -0.0141 -0.0669 0.1636 -0.0272 0.0735 -20.1949 65.6787 7.0916 20 0.8881 0.4368 -1.4804 7.263 5.8595 8.6805 -0.0983 -0.0057 0.1935 -0.3362 0.2665 0.2796 -0.1883 0.1859 -0.1682 0.128 0.0255 -0.0151 0.2312 -0.0089 0.1251 -23.2456 67.3201 16.7044 21 4.2621 2.6336 1.4907 6.1936 0.1932 1.7102 0.1065 -0.1244 0.2855 0.4896 -0.0831 0.1396 -0.1476 -0.0245 -0.0234 0.0753 -0.0123 0.024 0.1512 -0.0114 0.1235 -18.749 80.2856 16.8086 22 5.5955 2.3077 1.1017 12.7782 -1.0056 10.1427 0.04 0.9859 -0.5879 -1.0042 0.2678 0.3524 0.8129 -0.5577 -0.3077 0.3396 -0.0006 -0.0692 0.4065 -0.0613 0.294 35.5146 50.2053 10.9326 23 8.1385 0.7963 5.866 2.9647 -0.3062 7.7797 0.1562 -0.0246 -0.3645 0.1094 -0.0555 0.1014 0.2425 -0.0161 -0.1007 0.0906 -0.0017 0.0342 0.1061 -0.009 0.0966 47.0479 54.5667 24.7849 24 4.7321 0.5302 0.5322 0.2087 0.0055 0.1137 0.0654 -0.0783 0.2532 0.1217 -0.0489 0.134 -0.0521 -0.0617 -0.0166 0.1367 -0.0007 0.0323 0.147 -0.0129 0.1676 40.8125 61.3279 22.9318 25 2.0329 1.481 6.8339 8.5279 -3.5768 33.0706 -0.1954 -0.033 0.2898 -0.0297 0.4169 0.9217 -0.6934 -0.7214 -0.2215 0.0913 0.0165 0.0158 0.1983 0.0315 0.6487 30.0404 69.1925 24.1933 26 6.4813 -1.1042 -1.016 2.8349 -0.7371 4.9412 0.0795 -0.0556 0.4546 0.2012 -0.0002 0.1682 -0.1758 -0.1927 -0.0793 0.1081 -0.028 0.0208 0.0726 -0.0597 0.1449 47.7839 69.7635 25.3857 27 20.4307 4.2793 5.5639 10.4132 -1.7962 2.4488 -0.1147 0.5889 0.0089 -0.0927 -0.0049 -0.5098 -0.0131 0.1277 0.1196 0.2746 0.0269 0.0211 0.4042 0.0642 0.2422 37.787 66.7434 14.0126 28 5.8891 1.4094 1.7468 0.6948 0.4291 0.6093 -0.1665 0.2953 0.6118 -0.0832 0.0225 0.3091 -0.1405 -0.0214 0.144 0.2388 -0.007 -0.0118 0.271 0.0136 0.2524 33.572 67.3394 18.6478 29 4.4036 -1.8235 -0.8413 4.9419 1.8517 9.7787 0.1712 0.382 0.0264 -0.6986 0.0897 -0.251 0.208 0.4993 -0.2609 0.1671 -0.0076 0.0151 0.2309 -0.0556 0.1592 42.7381 39.1675 12.9476 30 2.0691 -1.5275 -0.3568 3.8452 1.7335 1.812 0.0232 -0.0928 0.0192 0.0451 0.0295 0.1208 -0.0063 -0.0289 -0.0527 0.0623 -0.0164 0.0206 0.1205 -0.0174 0.1089 31.0395 43.9502 24.0462 31 14.7605 -0.6869 -1.9162 1.4138 -2.3666 4.6208 -0.0597 -0.6954 -0.5651 0.0395 0.1827 0.1352 -0.0398 -0.222 -0.123 0.1927 -0.0412 -0.0115 0.2069 -0.0322 0.1959 33.4317 26.181 25.3951 32 4.6232 -3.9365 4.0178 9.4939 -0.9673 4.9338 0.0346 -0.4073 -0.1137 0.2919 -0.0387 0.5433 -0.0158 -0.4516 0.004 0.0852 -0.0216 0.0758 0.1623 0.0102 0.2176 21.5953 41.9049 27.3639 33 9.3527 -9.5938 -6.3082 10.2926 4.4633 13.3536 0.2114 0.0943 -0.5773 -0.3648 -0.1212 0.7135 0.1545 -0.324 -0.0902 0.1468 0.0401 -0.0946 0.2239 -0.0387 0.3963 18.2999 39.8006 18.6213 34 35.6305 -7.272 2.8785 8.0411 -1.7802 0.4796 0.0683 0.6047 0.7818 -0.4583 -0.0439 0.0603 0.0957 -0.0486 -0.0244 0.1803 0.0324 -0.059 0.2965 0.0299 0.1777 31.5448 31.2017 14.6942 35 7.0218 -4.988 -2.0841 5.0906 2.8794 2.7884 0.1554 0.3734 -0.3872 -0.0679 -0.2565 0.451 0.1499 -0.2011 0.1011 0.0871 -0.0513 -0.0013 0.0747 0.0024 0.1677 29.2853 28.5612 18.9428 36 1.5008 1.399 4.6063 5.555 -0.9924 21.3789 -0.1985 -0.0541 0.0996 -1.0428 0.0161 -0.0495 -0.2508 -0.6356 0.1824 0.6515 0.235 0.173 0.5006 0.1632 0.5382 49.5484 53.5836 9.8672 37 3.8458 2.5819 -0.8761 9.3644 -6.5444 8.2935 0.0735 -0.0216 0.0647 0.2672 0.1679 0.1368 -0.1572 -0.2893 -0.2414 0.0837 0.0235 0.0013 0.133 -0.042 0.0842 48.7257 40.2187 23.1537 38 1.7354 1.659 0.1764 5.4293 0.3901 0.0319 0.0439 -0.2047 -0.1176 0.0211 -0.0206 -0.3645 0.0022 -0.0212 -0.0233 0.1033 -0.0105 -0.0169 0.1333 0.0052 0.1026 57.9768 42.5108 22.6135 39 11.7104 -11.5495 3.1837 14.4752 -3.4856 17.4419 -0.1522 -0.3336 -0.0998 0.1817 0.0789 -0.31 0.3047 0.7978 0.0734 0.2055 -0.0218 -0.0269 0.2486 -0.049 0.254 68.933 45.6321 25.9555 40 4.6899 2.395 -0.1833 8.13 3.0397 7.0521 -0.0329 -0.3294 -0.1576 0.2941 0.0605 -0.4024 0.1405 0.26 -0.0277 0.0888 0.0104 -0.1058 0.1036 0.0279 0.1438 59.9633 30.3059 25.5102 41 0.1597 1.0757 0.1376 10.2646 1.598 2.8178 -0.0159 0.0827 -0.1408 -0.3618 0.0281 -0.5565 -0.1111 0.1362 -0.0122 0.0976 0.0173 0.0412 0.2207 -0.069 0.2984 63.9286 46.5079 16.2101 42 2.799 4.9762 -2.2668 11.2752 -7.7847 7.7794 -0.0802 0.0948 -0.5389 -0.4161 -0.3402 -1.011 0.27 0.7751 0.4204 0.2395 0.032 0.1264 0.1407 -0.0556 0.3601 66.7168 39.3194 19.2569
精密化 TLSグループ 大きな表を表示 (5 x 42) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A1 - 10 2 X-RAY DIFFRACTION 2 A11 - 41 3 X-RAY DIFFRACTION 3 A42 - 53 4 X-RAY DIFFRACTION 4 A54 - 59 5 X-RAY DIFFRACTION 5 A60 - 76 6 X-RAY DIFFRACTION 6 A77 - 90 7 X-RAY DIFFRACTION 7 A91 - 100 8 X-RAY DIFFRACTION 8 B3 - 12 9 X-RAY DIFFRACTION 9 B13 - 22 10 X-RAY DIFFRACTION 10 B23 - 47 11 X-RAY DIFFRACTION 11 B48 - 61 12 X-RAY DIFFRACTION 12 B62 - 76 13 X-RAY DIFFRACTION 13 B77 - 90 14 X-RAY DIFFRACTION 14 B91 - 100 15 X-RAY DIFFRACTION 15 C1 - 10 16 X-RAY DIFFRACTION 16 C11 - 43 17 X-RAY DIFFRACTION 17 C44 - 53 18 X-RAY DIFFRACTION 18 C54 - 59 19 X-RAY DIFFRACTION 19 C60 - 73 20 X-RAY DIFFRACTION 20 C74 - 80 21 X-RAY DIFFRACTION 21 C81 - 100 22 X-RAY DIFFRACTION 22 D1 - 11 23 X-RAY DIFFRACTION 23 D12 - 27 24 X-RAY DIFFRACTION 24 D28 - 52 25 X-RAY DIFFRACTION 25 D53 - 57 26 X-RAY DIFFRACTION 26 D58 - 78 27 X-RAY DIFFRACTION 27 D79 - 83 28 X-RAY DIFFRACTION 28 D84 - 100 29 X-RAY DIFFRACTION 29 E1 - 15 30 X-RAY DIFFRACTION 30 E16 - 46 31 X-RAY DIFFRACTION 31 E47 - 60 32 X-RAY DIFFRACTION 32 E61 - 72 33 X-RAY DIFFRACTION 33 E73 - 78 34 X-RAY DIFFRACTION 34 E79 - 85 35 X-RAY DIFFRACTION 35 E86 - 100 36 X-RAY DIFFRACTION 36 F1 - 8 37 X-RAY DIFFRACTION 37 F9 - 28 38 X-RAY DIFFRACTION 38 F29 - 53 39 X-RAY DIFFRACTION 39 F54 - 59 40 X-RAY DIFFRACTION 40 F60 - 76 41 X-RAY DIFFRACTION 41 F77 - 90 42 X-RAY DIFFRACTION 42 F91 - 100