ソフトウェア 名称 バージョン 分類 NB REFMAC5.5.0109精密化 Show PDB_EXTRACT3.1 データ抽出 Show SBC-Collectデータ収集 HKL-3000データ削減 HKL-3000データスケーリング HKL-3000位相決定 MLPHARE位相決定 直接法位相決定 SHELXDE位相決定 RESOLVE位相決定 ARP/wARPモデル構築 Cootモデル構築 CNS位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 2.99→50 Å / Cor.coef. Fo :Fc : 0.934 / Cor.coef. Fo :Fc free : 0.903 / Occupancy max : 1 / Occupancy min : 0.75 / SU B : 25.238 / SU ML : 0.206 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R Free : 0.3 立体化学のターゲット値 : MAXIMUM LIKELIHOOD WITH PHASES詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDEDRfactor 反射数 %反射 Selection details Rfree 0.2157 1166 5.2 % RANDOM Rwork 0.1757 - - - all 0.1778 22578 - - obs 0.1778 22578 97.56 % -
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 : 1.4 Å / 溶媒モデル : MASK原子変位パラメータ Biso max : 132.6 Å2 / Biso mean : 39.9018 Å2 / Biso min : 18.59 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.73 Å2 0.37 Å2 0 Å2 2- - 0.73 Å2 0 Å2 3- - - -1.1 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.99→50 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4266 0 2 125 4393
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.011 0.022 4338 X-RAY DIFFRACTION r_angle_refined_deg1.287 1.933 5847 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.23 5 519 X-RAY DIFFRACTION r_dihedral_angle_2_deg37.765 25.702 228 X-RAY DIFFRACTION r_dihedral_angle_3_deg16.692 15 822 X-RAY DIFFRACTION r_dihedral_angle_4_deg14.826 15 16 X-RAY DIFFRACTION r_chiral_restr0.093 0.2 650 X-RAY DIFFRACTION r_gen_planes_refined0.003 0.02 3242 X-RAY DIFFRACTION r_mcbond_it1.429 1.5 2588 X-RAY DIFFRACTION r_mcangle_it2.671 2 4197 X-RAY DIFFRACTION r_scbond_it2.41 3 1750 X-RAY DIFFRACTION r_scangle_it4.269 4.5 1650 X-RAY DIFFRACTION r_rigid_bond_restr1.233 3 4338
LS精密化 シェル 解像度 : 2.992→3.069 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.268 69 - Rwork 0.236 1292 - all - 1361 - obs - 1361 86.47 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 20) 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 0.247 -0.734 0.2525 0.623 -0.1521 0.8103 0.0911 0.0269 -0.0281 -0.1844 0.0374 0.0241 0.0162 0.0411 -0.1285 0.2245 0.007 -0.0116 0.1708 -0.0042 0.2753 57.889 42.632 7.86 2 2.136 0.2767 1.5841 7.7713 -1.6352 3.0565 0.0558 -0.1348 0.1565 -0.0063 0.034 -0.0283 -0.0939 0.1184 -0.0899 0.1507 0.0197 0.012 0.1687 0.0048 0.2298 70.073 51.519 19.515 3 -0.2925 -0.4589 0.2894 3.4722 1.6741 1.7038 0.0548 -0.027 0.1012 -0.3501 -0.0296 -0.0617 -0.1008 0.0063 -0.0253 0.2093 0.0217 -0.0011 0.1932 0.0068 0.2302 64.401 50.666 5.226 4 0.3893 0.3764 0.1872 -0.0768 0.4267 0.0904 -0.0117 -0.031 -0.006 -0.0408 0.0139 0.0496 -0.0094 -0.0059 -0.0022 0.188 0.0343 0.0093 0.1718 -0.0091 0.2565 56.215 54.172 19.5 5 0.4858 -0.2824 1.5394 1.575 -1.4082 3.4199 0.0817 0.1028 0.0355 -0.2609 -0.1397 0.0133 0.1815 0.1756 0.058 0.1934 0.0584 0.0031 0.1696 0.0142 0.2593 52.175 56.048 17.415 6 -0.0764 0.1241 0.2166 -2.0528 1.9948 -0.4021 0.0036 0.0442 0.0353 -0.0165 0.1456 0.1958 0.0649 -0.2478 -0.1492 0.2426 0.0433 -0.0016 0.2163 0.0402 0.3343 44.965 51.586 20.818 7 0.8189 -0.1583 0.4495 1.1773 0.1486 0.7206 -0.073 -0.0337 0.0216 -0.0311 0.0643 0.1471 0.0152 -0.0894 0.0087 0.1813 0.0213 -0.0222 0.1786 0.0031 0.2965 39.108 51.621 17.041 8 4.0962 -0.7599 4.5809 3.7456 -4.425 7.5794 0.3688 0.1408 -0.4526 -0.0707 0.113 0.4234 0.3044 0.058 -0.4818 0.168 0.044 -0.083 0.1741 -0.0066 0.3646 40.801 34.869 9.317 9 1.9934 -1.3444 1.6393 0.1512 -0.5157 0.2685 -0.1018 0.0549 0.1799 -0.1601 0.0411 0.0783 -0.0192 -0.0336 0.0607 0.2797 0.0354 -0.0827 0.1468 0.0676 0.3386 41.648 44.741 7.412 10 1.3561 -0.3773 1.536 3.0966 -1.8384 1.3837 -0.0154 0.1116 -0.1082 -0.2012 -0.0098 0.2555 0.2161 0.0192 0.0252 0.2011 0.0118 -0.0753 0.1711 -0.0197 0.3336 49.104 40.656 4.651 11 0.7002 0.1898 0.0871 0.182 -0.152 1.1394 -0.0232 -0.1346 -0.0236 0.015 0.1222 -0.1343 0.1113 0.3209 -0.099 0.1676 0.0122 -0.0153 0.2547 -0.0418 0.2868 72.829 66.584 45.812 12 1.7772 3.5466 -3.0503 6.058 -1.6673 10.4796 0.0029 -0.0339 0.1095 -0.1306 0.0251 -0.0542 -0.0067 0.1771 -0.028 0.1361 0.0525 0.014 0.1695 -0.0054 0.2792 72.605 53.129 32.669 13 0.7756 0.5287 1.5691 0.7195 0.247 4.1311 0.0711 -0.1398 -0.1683 0.1247 0.0004 0.0371 0.3456 0.2796 -0.0715 0.1623 0.0474 0.0043 0.2422 -0.0098 0.2659 72.828 56.09 47.77 14 0.0427 -0.2807 -0.3435 0.3248 -0.108 1.2142 0.0597 -0.1018 0.042 -0.0031 0.0098 -0.0213 -0.0271 0.1324 -0.0696 0.1733 0.0008 -0.0069 0.1904 -0.0228 0.2544 61.37 60.682 36.006 15 0.2211 0.0448 0.0641 1.3409 -1.0927 2.9386 0.0417 -0.1353 -0.0467 0.1956 -0.0275 0.0669 -0.2826 0.1243 -0.0141 0.1834 0.022 -0.0281 0.1994 0.0052 0.2684 57.557 61.891 39.578 16 -0.4069 -0.418 1.0649 -0.5387 0.7248 -0.156 -0.0252 -0.0569 0.0494 -0.0087 0.0989 0.0514 -0.122 -0.0946 -0.0737 0.2076 0.0121 -0.0023 0.2187 0.0071 0.281 54.546 69.81 37.613 17 0.6931 0.2786 -0.2534 0.6375 0.4659 0.6959 0.0074 -0.0084 0.031 0.0298 0.0501 -0.0115 -0.0485 0.0391 -0.0575 0.1631 0.006 0.0086 0.1794 -0.0019 0.2619 51.343 73.469 42.39 18 3.1135 2.2188 -3.3422 2.6455 -2.6377 3.1529 0.0356 -0.0077 0.1353 0.0896 0.0582 0.0242 -0.0697 -0.1117 -0.0938 0.1709 -0.0162 0.001 0.2474 -0.0493 0.2767 68.682 86.448 45.068 19 -0.4623 -0.1 0.2176 0.4847 0.2342 -0.1462 0.0685 -0.0269 0.1004 0.115 0.0571 -0.0633 -0.0266 0.0864 -0.1257 0.1769 -0.0157 0.0173 0.2345 -0.0325 0.2814 60.181 76.026 50.385 20 1.8374 0.4358 -0.3784 2.2647 0.1968 0.6166 0.1928 -0.1713 0.2049 0.1965 0.004 -0.1309 -0.0927 0.2047 -0.1968 0.1549 0.0117 0.0084 0.228 -0.0572 0.254 68.991 73.912 50.793
精密化 TLSグループ 大きな表を表示 (5 x 20) 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 - 41 2 X-RAY DIFFRACTION 2 A42 - 57 3 X-RAY DIFFRACTION 3 A58 - 78 4 X-RAY DIFFRACTION 4 A79 - 113 5 X-RAY DIFFRACTION 5 A114 - 131 6 X-RAY DIFFRACTION 6 A132 - 151 7 X-RAY DIFFRACTION 7 A152 - 198 8 X-RAY DIFFRACTION 8 A199 - 221 9 X-RAY DIFFRACTION 9 A222 - 244 10 X-RAY DIFFRACTION 10 A245 - 263 11 X-RAY DIFFRACTION 11 B1 - 41 12 X-RAY DIFFRACTION 12 B42 - 57 13 X-RAY DIFFRACTION 13 B58 - 78 14 X-RAY DIFFRACTION 14 B79 - 113 15 X-RAY DIFFRACTION 15 B114 - 131 16 X-RAY DIFFRACTION 16 B132 - 151 17 X-RAY DIFFRACTION 17 B152 - 198 18 X-RAY DIFFRACTION 18 B199 - 221 19 X-RAY DIFFRACTION 19 B222 - 244 20 X-RAY DIFFRACTION 20 B245 - 263