ソフトウェア 名称 バージョン 分類 Aimless0.3.11データスケーリング PHENIXdev_2203精密化 PDB_EXTRACT3.2 データ抽出 xia20.3.7.0データ削減 PHENIXdev_1839位相決定 PHASER2.6.1位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 1.55→22 Å / SU ML : 0.16 / 交差検証法 : THROUGHOUT / σ(F) : 1.34 / 位相誤差 : 19.51 Rfactor 反射数 %反射 Rfree 0.2057 1959 4.92 % Rwork 0.1713 - - obs 0.173 39821 99.8 %
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å原子変位パラメータ Biso max : 128.2 Å2 / Biso mean : 28.4863 Å2 / Biso min : 7.26 Å2 精密化ステップ サイクル : final / 解像度 : 1.55→22 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2578 0 0 227 2805 Biso mean - - - 32.89 - 残基数 - - - - 313
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.017 2766 X-RAY DIFFRACTION f_angle_d1.525 3776 X-RAY DIFFRACTION f_chiral_restr0.104 443 X-RAY DIFFRACTION f_plane_restr0.01 492 X-RAY DIFFRACTION f_dihedral_angle_d17.636 1742
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / 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 (%)1.55-1.5888 0.2977 113 0.2342 2697 2810 100 1.5888-1.6317 0.2587 138 0.2226 2653 2791 100 1.6317-1.6797 0.223 146 0.2083 2675 2821 100 1.6797-1.7339 0.2359 135 0.1977 2678 2813 100 1.7339-1.7959 0.2247 161 0.1871 2642 2803 100 1.7959-1.8677 0.2377 129 0.1823 2679 2808 100 1.8677-1.9527 0.2104 115 0.1805 2724 2839 100 1.9527-2.0556 0.2148 138 0.1764 2680 2818 100 2.0556-2.1843 0.2079 159 0.1602 2691 2850 100 2.1843-2.3527 0.1975 168 0.1606 2679 2847 100 2.3527-2.5892 0.2106 149 0.1691 2695 2844 100 2.5892-2.963 0.2236 134 0.1718 2733 2867 100 2.963-3.7302 0.1746 122 0.1523 2768 2890 99 3.7302-22.0036 0.1848 152 0.1623 2868 3020 99
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 25) 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 6.9347 -4.5202 -5.2899 5.7761 5.1522 6.4464 0.0788 0.4236 -0.0757 -0.0144 0.0333 -0.2982 0.1434 -0.3118 -0.1454 0.4006 0.0029 -0.0429 0.1688 -0.0199 0.271 48.9118 4.4752 43.9478 2 3.3223 1.8546 0.0231 5.7859 0.6787 3.7531 0.1317 0.0335 0.0664 0.0388 -0.1237 0.3322 -0.0717 -0.3672 -0.0519 0.0684 0.0029 -0.0059 0.1215 -0.0046 0.0555 40.5816 21.7433 49.9864 3 3.0271 -2.5518 1.1219 4.9428 -0.733 2.7325 0.1631 0.0259 0.1191 -0.1173 -0.1227 -0.4013 0.0001 0.2397 -0.0547 0.0753 -0.001 0.0251 0.0989 -0.009 0.0819 50.7202 21.3602 50.102 4 7.1292 -2.9637 -2.9399 5.336 5.0592 7.4135 0.0813 -0.1584 0.12 -0.0867 -0.1895 0.0958 -0.1348 0.0746 0.0428 0.1719 -0.011 -0.0339 0.1918 0.0298 0.1601 52.0804 16.7974 60.5007 5 1.6676 1.6459 1.3951 5.2839 3.4329 3.3011 -0.1332 0.1031 0.1791 0.0322 0.144 -0.1744 -0.4148 -0.0163 -0.0028 0.1735 0.0188 -0.0063 0.151 0.0094 0.1651 45.8884 57.2121 35.1923 6 3.2003 2.0077 1.5622 2.9272 1.3917 3.3844 -0.0397 0.0531 0.0389 -0.1522 -0.018 0.0156 0.0424 0.1397 0.0578 0.0512 0.0094 0.0095 0.0841 -0.0032 0.0846 51.3591 45.5359 31.9243 7 3.4448 -0.1809 -1.5953 0.8876 -2.0735 6.4853 0.3061 0.8014 1.1345 -0.3328 0.1292 -1.319 -1.482 0.3281 -0.1804 0.4098 -0.034 0.1062 0.41 0.1318 0.6267 56.8525 55.2273 25.2256 8 3.2057 -2.2152 2.809 3.142 -4.0357 5.2079 -0.2881 0.1438 0.478 -0.7565 -0.0408 -0.0975 -0.3456 0.1995 0.3711 0.404 0.0655 -0.0495 0.2138 0.0608 0.2682 42.0843 64.0384 31.6878 9 3.0362 1.5833 -0.133 5.661 -0.9124 3.5635 0.0719 -0.08 0.1366 0.2355 -0.0718 -0.1547 -0.0452 -0.0795 -0.025 0.082 -0.0231 -0.0128 0.0962 0.0049 0.1017 52.7077 48.9279 43.449 10 5.1348 -5.1472 1.8933 6.0102 -2.3014 1.6611 0.0309 0.0937 0.068 0.0511 -0.045 -0.018 0.0157 -0.1908 -0.0619 0.0739 0.0105 0.0217 0.1209 -0.0017 0.0931 43.8182 46.7947 40.3492 11 2.4608 -1.8292 -2.5214 1.4037 2.0443 3.3593 0.3337 -0.6564 0.5686 0.0314 -0.0213 -0.2282 -0.1468 0.4169 -0.1988 0.1656 -0.029 0.012 0.2318 -0.0064 0.2079 23.5609 57.8442 45.3757 12 4.313 -1.3026 2.119 2.6778 -1.2593 1.2089 0.1047 -0.9148 -0.2896 0.6246 0.2552 0.1838 0.5318 -0.2865 0.2975 0.5148 -0.0267 -0.0077 0.2203 0.0206 0.1562 41.0497 5.1871 47.8119 13 6.4751 3.4667 1.3512 2.6041 0.4516 2.0769 -0.1346 0.1681 -0.0654 -0.5347 0.1672 -0.0751 0.492 0.2844 -0.0351 0.2138 0.0522 0.0356 0.1397 0.0107 0.1239 53.6139 15.089 40.7771 14 3.6099 -3.0265 -3.0736 6.5883 -2.4298 8.8057 0.2873 -0.2348 0.7528 -0.1515 -0.1581 -1.1095 -0.2729 0.7475 0.0035 0.1375 -0.0291 0.0452 0.1277 -0.0251 0.2075 55.1563 28.7068 38.2891 15 6.0558 4.61 -0.5997 4.2842 -0.1671 2.704 0.0147 0.011 -0.1997 -0.1569 0.04 -0.1537 0.1529 -0.1038 -0.067 0.1445 -0.0043 -0.0197 0.1029 -0.0001 0.0891 44.4535 21.2778 40.1878 16 8.6573 1.3075 1.2502 6.2411 -0.4757 6.1529 0.2031 0.2684 0.3765 -0.2885 -1.1472 -1.3565 -0.6278 1.0552 0.7615 0.5688 -0.1319 -0.0398 0.6464 0.1373 0.5837 29.5608 9.5927 39.0065 17 5.9831 0.7004 2.4142 1.4785 -0.097 1.0697 0.3328 -0.5293 0.4117 0.6907 0.5501 0.0196 -0.1344 0.1615 1.6006 0.563 -0.0211 0.0933 0.3383 -0.1321 0.2358 43.483 65.5487 60.5151 18 6.9556 1.0104 0.0044 7.286 -0.8454 5.6126 -0.1441 0.0133 0.2967 0.0234 0.0731 -0.0767 -0.4077 -0.034 0.0897 0.1375 0.0195 0.0154 0.1154 0.0199 0.1075 38.9444 53.1914 49.8124 19 6.9875 -5.2791 6.8175 4.1185 -4.9441 7.0195 0.2414 -0.3415 -0.4308 -0.1707 0.1654 0.5326 0.5584 -0.7546 -0.2288 0.1464 -0.0011 0.0141 0.1398 0.0073 0.1501 40.6727 39.1167 48.5836 20 3.723 3.1265 1.8273 4.1818 3.3317 4.6293 0.0079 -0.3036 0.2878 0.168 -0.0895 0.297 -0.0886 0.2303 0.0259 0.1022 -0.0152 0.0242 0.1462 -0.0293 0.1062 46.6908 48.6501 55.4213 21 3.2432 5.3275 -3.4605 9.3082 -4.4438 5.707 -0.8188 1.5239 -0.6777 -1.2218 1.0711 -0.3475 -0.0778 -0.9712 -0.7503 0.6932 -0.2012 0.0413 0.7311 0.021 1.0688 57.9295 73.7366 52.9502 22 5.8872 -0.0856 1.4202 4.4581 4.1548 4.2841 -0.0737 0.4153 -0.2898 -0.6645 0.6186 -0.2898 1.3251 0.1696 0.1001 0.7382 -0.0037 -0.0045 0.2247 -0.0779 0.2626 46.7535 1.1514 16.3921 23 7.4837 -3.3384 -0.9738 6.8489 1.5956 6.4943 -0.23 -0.2268 0.0781 0.0378 0.3152 -0.2832 0.3973 0.0179 -0.0995 0.2368 -0.0209 -0.0269 0.2036 -0.0084 0.1355 41.7554 14.885 30.0277 24 6.267 5.6389 -6.1486 6.3838 -6.0951 6.3044 0.0146 0.3098 0.3296 -0.1845 0.2878 0.7799 0.171 -0.4545 -0.2423 0.2148 0.0204 -0.0203 0.1067 0.0074 0.1371 43.7538 28.7705 32.2118 25 4.0856 -1.8126 -2.1973 3.8106 3.8831 5.6059 0.0223 0.1467 -0.3167 0.1033 -0.1616 0.0189 0.1717 0.0488 -0.0179 0.1454 0.0327 -0.0454 0.1265 -0.016 0.1054 50.3819 18.881 24.2148
精密化 TLSグループ 大きな表を表示 (6 x 25) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 7 )A1 - 7 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 8 through 24 )A8 - 24 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 25 through 40 )A25 - 40 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 41 through 52 )A41 - 52 5 X-RAY DIFFRACTION 5 chain 'B' and (resid -2 through 19 ) B-2 - 19 6 X-RAY DIFFRACTION 6 chain 'B' and (resid 20 through 40 )B20 - 40 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 41 through 50 )B41 - 50 8 X-RAY DIFFRACTION 8 chain 'C' and (resid -1 through 7 ) C-1 - 7 9 X-RAY DIFFRACTION 9 chain 'C' and (resid 8 through 24 )C8 - 24 10 X-RAY DIFFRACTION 10 chain 'C' and (resid 25 through 40 )C25 - 40 11 X-RAY DIFFRACTION 11 chain 'C' and (resid 41 through 52 )C41 - 52 12 X-RAY DIFFRACTION 12 chain 'D' and (resid 1 through 7 )D1 - 7 13 X-RAY DIFFRACTION 13 chain 'D' and (resid 8 through 19 )D8 - 19 14 X-RAY DIFFRACTION 14 chain 'D' and (resid 20 through 24 )D20 - 24 15 X-RAY DIFFRACTION 15 chain 'D' and (resid