ソフトウェア 名称 バージョン 分類 Aimless0.2.17データスケーリング PHENIX1.8.4_1496精密化 PDB_EXTRACT3.2 データ抽出 XDSデータ削減 MOLREP位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 2DVY解像度 : 1.9→43.619 Å / SU ML : 0.22 / 交差検証法 : FREE R-VALUE / σ(F) : 1.33 / 位相誤差 : 27.83 Rfactor 反射数 %反射 Rfree 0.2481 2444 4.96 % Rwork 0.2062 - - obs 0.2083 49246 99.25 %
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 : 170.78 Å2 / Biso mean : 60.99 Å2 / Biso min : 25.51 Å2 精密化ステップ サイクル : final / 解像度 : 1.9→43.619 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3475 407 0 162 4044 Biso mean - - - 53.7 - 残基数 - - - - 448
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.013 4000 X-RAY DIFFRACTION f_angle_d1.296 5485 X-RAY DIFFRACTION f_chiral_restr0.063 613 X-RAY DIFFRACTION f_plane_restr0.006 624 X-RAY DIFFRACTION f_dihedral_angle_d16.685 1553
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 17
大きな表を表示 (7 x 17) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.9-1.9388 0.34 146 0.3407 2677 2823 99 1.9388-1.981 0.3599 143 0.2899 2762 2905 100 1.981-2.027 0.3203 137 0.273 2743 2880 100 2.027-2.0777 0.2841 141 0.2555 2723 2864 100 2.0777-2.1339 0.26 123 0.2447 2738 2861 100 2.1339-2.1967 0.2846 150 0.2351 2738 2888 100 2.1967-2.2676 0.2784 159 0.2409 2741 2900 100 2.2676-2.3486 0.2619 142 0.2443 2726 2868 99 2.3486-2.4427 0.2297 132 0.2296 2754 2886 100 2.4427-2.5538 0.2816 127 0.2375 2758 2885 100 2.5538-2.6884 0.3162 146 0.2469 2765 2911 100 2.6884-2.8569 0.2797 157 0.2457 2736 2893 100 2.8569-3.0774 0.2497 147 0.2283 2784 2931 100 3.0774-3.387 0.2481 144 0.2038 2766 2910 99 3.387-3.8768 0.2574 171 0.1869 2787 2958 100 3.8768-4.8833 0.2039 141 0.1564 2829 2970 100 4.8833-43.6308 0.2113 138 0.1854 2775 2913 93
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 9) 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 1.0343 -0.7817 1.5432 3.4318 -1.0624 5.6842 0.1361 -0.0249 0 -0.2787 -0.0398 0.1019 -0.0804 -0.1987 -0.0903 0.2901 0.0548 0.0843 0.3378 -0.0059 0.2119 -24.3926 -57.6118 4.8182 2 1.2009 -1.5456 -0.0549 8.855 -0.5088 -0.0003 -0.0805 0.1908 0.3102 0.0042 0.111 -1.4604 -0.3369 -0.0095 -0.0327 0.3722 -0.0581 0.0586 0.4437 0.0343 0.5171 -6.196 -37.302 10.5346 3 2.4694 -0.2944 1.3204 2.0022 -0.271 6.0742 0.1339 -0.0155 0.0926 -0.1003 -0.0061 -0.0125 -0.3063 -0.1574 -0.0626 0.2605 0.0653 0.0945 0.2976 0.0081 0.2016 -21.2587 -55.6047 7.692 4 3.6102 1.1896 -1.2633 6.857 -2.1572 5.7965 0.5346 -0.2083 0.6729 0.4183 -0.1846 0.4884 -1.0653 0.1023 -0.2124 0.6581 -0.107 0.1329 0.4165 -0.0285 0.6061 -19.9749 -15.0786 19.4712 5 1.6181 0.0849 -1.5985 5.943 -0.3445 2.6132 0.2058 0.3402 0.1533 -1.261 -0.2513 -0.481 -0.2527 -0.1115 0.0117 0.4122 -0.0303 0.0911 0.413 0.0226 0.449 -7.9226 -36.6073 5.0574 6 3.3798 -2.6042 -3.9908 3.2746 1.504 6.7998 0.6713 0.009 0.2156 0.2213 -0.6888 0.0068 -0.173 -0.2743 0.1001 0.482 -0.0427 0.0581 0.4534 0.0939 0.511 -16.32 -24.0711 13.6859 7 3.2447 1.0273 -2.3223 5.4987 -3.3041 3.9759 0.8191 -0.4241 0.7521 0.1356 -0.4417 0.2545 -1.078 0.2103 -0.2272 0.6617 -0.1058 0.1172 0.4255 0.0041 0.6774 -19.2866 -13.6088 17.0527 8 8.8836 -0.4296 -5.9341 2.8666 0.5984 3.9396 0.2222 0.1443 0.1646 0.6578 0.2786 0.0476 0.4307 -0.0906 -0.4524 0.6756 -0.1341 0.0363 0.4579 -0.0534 0.3236 -35.9668 -33.74 32.0831 9 3.8912 -3.4397 2.8035 7.8667 -5.7742 4.2655 -0.074 -0.2059 0.2756 -0.8449 0.5261 -0.1515 0.1262 -0.3003 -0.4412 0.5349 0.0436 0.047 0.5372 -0.0509 0.2681 -37.8119 -34.1899 0.2916
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 8 through 105 )A8 - 105 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 106 through 140 )A106 - 140 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 141 through 223 )A141 - 223 4 X-RAY DIFFRACTION 4 chain 'B' and (resid 8 through 105 )B8 - 105 5 X-RAY DIFFRACTION 5 chain 'B' and (resid 106 through 140 )B106 - 140 6 X-RAY DIFFRACTION 6 chain 'B' and (resid 141 through 172 )B141 - 172 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 173 through 223 )B173 - 223 8 X-RAY DIFFRACTION 8 chain 'C' and (resid 1 through 10 )C1 - 10 9 X-RAY DIFFRACTION 9 chain 'C' and (resid 11 through 20 )C11 - 20