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 PHENIX精密化 Show PDB_EXTRACT3.22 データ抽出 Show XDSデータ削減 MoRDa位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 4DHE解像度 : 1.8→48.204 Å / SU ML : 0.2 / 交差検証法 : FREE R-VALUE / σ(F) : 1.35 / 位相誤差 : 18.11 Rfactor 反射数 %反射 Rfree 0.2071 2046 4.78 % Rwork 0.1672 - - obs 0.1691 42797 99.88 %
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 : 85.42 Å2 / Biso mean : 23.7496 Å2 / Biso min : 7.13 Å2 精密化ステップ サイクル : final / 解像度 : 1.8→48.204 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2905 0 54 319 3278 Biso mean - - 40.55 33.66 - 残基数 - - - - 373
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.006 3074 X-RAY DIFFRACTION f_angle_d0.818 4181 X-RAY DIFFRACTION f_chiral_restr0.052 477 X-RAY DIFFRACTION f_plane_restr0.005 532 X-RAY DIFFRACTION f_dihedral_angle_d12.475 1846
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0 / Total num. of bins used : 15 / % reflection obs : 100 %
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all 1.8001-1.842 0.2751 152 0.2446 2615 2767 1.842-1.888 0.2515 121 0.2147 2692 2813 1.888-1.9391 0.2363 145 0.187 2660 2805 1.9391-1.9962 0.2338 133 0.1773 2693 2826 1.9962-2.0606 0.2357 117 0.1773 2700 2817 2.0606-2.1342 0.2111 131 0.1683 2685 2816 2.1342-2.2197 0.1834 143 0.1634 2710 2853 2.2197-2.3207 0.2066 120 0.1538 2697 2817 2.3207-2.4431 0.2402 126 0.1598 2726 2852 2.4431-2.5961 0.2006 146 0.162 2702 2848 2.5961-2.7965 0.2082 142 0.1715 2692 2834 2.7965-3.0779 0.2153 152 0.1701 2731 2883 3.0779-3.5232 0.2073 141 0.1639 2745 2886 3.5232-4.4384 0.18 138 0.1449 2791 2929 4.4384-48.2208 0.187 139 0.1701 2912 3051
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 10) 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 2.507 -0.1964 -0.2885 2.3745 -1.8778 4.0353 -0.0996 0.053 -0.0075 -0.2471 -0.1491 -0.3461 -0.0824 0.4764 0.1764 0.1772 -0.0154 0.0231 0.1747 0.0329 0.1628 -2.5967 3.0091 10.6273 2 5.1774 1.709 3.8348 2.9974 1.9581 3.4164 -0.0195 -0.1874 0.5165 0.0208 -0.094 -0.261 -0.4077 -0.0334 0.0997 0.1502 -0.0112 0.0141 0.1514 -0.0204 0.1733 -8.1723 12.093 21.7633 3 1.0761 0.5505 -0.5065 2.0511 -0.941 1.4826 -0.0276 -0.0196 -0.1088 -0.1414 -0.0978 -0.1577 0.1515 0.0379 0.0693 0.0823 0.0104 0.0033 0.1108 0.0022 0.1016 -12.4925 -5.8561 19.8993 4 2.3058 -0.4977 -0.052 3.6374 -1.6907 1.7983 -0.0154 0.1282 -0.0855 -0.0179 0.0088 0.3841 0.0773 -0.1893 -0.0296 0.0997 -0.021 0.0206 0.116 -0.0354 0.1821 -37.7803 6.1274 38.9302 5 2.4043 -1.0692 -0.498 3.5415 -3.0876 3.6932 0.0729 0.0008 -0.1941 0.2094 0.1661 0.8153 -0.0006 -0.2914 -0.0086 0.1317 -0.022 0.0705 0.1612 -0.0067 0.2312 -41.1116 0.8454 44.4171 6 1.8483 -0.456 -0.1197 3.1532 0.4439 2.0219 0.0562 0.1947 -0.2525 0.0852 -0.0978 0.2903 0.3329 -0.1776 0.0342 0.1015 -0.0233 -0.0013 0.1605 -0.0242 0.1394 -33.9957 -1.7382 34.7331 7 1.0515 -1.0256 0.4597 7.6623 -3.5544 3.2009 0.0425 -0.0538 0.0045 0.1313 -0.1132 -0.1534 0.0171 0.0486 0.0671 0.0674 -0.0155 0.0302 0.1022 -0.0307 0.0789 -28.9483 -1.1155 42.7512 8 1.0694 0.2758 -0.8706 1.6162 -0.9537 3.6147 0.0586 -0.0148 -0.0422 0.1848 -0.0901 0.04 0.1194 0.0157 0.0214 0.0775 -0.0196 0.0023 0.1063 -0.0081 0.0915 -25.2172 -5.3429 43.7652 9 5.2103 3.2891 -5.1653 4.4368 -4.8164 7.4402 0.1222 -0.3065 -0.122 0.2705 -0.2796 -0.2822 -0.0584 0.5864 0.1715 0.1544 -0.0396 -0.068 0.1579 0.0029 0.1676 -19.0617 -8.0715 52.9001 10 1.8625 -0.2136 -0.0498 2.9864 -0.687 2.6414 -0.0448 -0.1147 0.0664 0.6452 0.0309 0.1659 -0.2521 -0.067 -0.0324 0.2376 -0.0248 0.0222 0.1454 -0.0352 0.1229 -28.3969 4.0499 52.1652
精密化 TLSグループ ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 2 through 75 )A2 - 75 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 76 through 102 )A76 - 102 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 103 through 201 )A103 - 201 4 X-RAY DIFFRACTION 4 chain 'B' and (resid 2 through 32 )B2 - 32 5 X-RAY DIFFRACTION 5 chain 'B' and (resid 33 through 66 )B33 - 66 6 X-RAY DIFFRACTION 6 chain 'B' and (resid 67 through 102 )B67 - 102 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 103 through 117 )B103 - 117 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 118 through 148 )B118 - 148 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 149 through 168 )B149 - 168 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 169 through 200 )B169 - 200