ソフトウェア 名称 バージョン 分類 SBC-Collectデータ収集 HKL-3000データ収集 HKL-3000位相決定 SHELXS位相決定 MLPHARE位相決定 直接法モデル構築 PHENIX(phenix.refine: dev_1745)精密化 HKL-3000データ削減 HKL-3000データスケーリング 直接法位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 1.8515→28.329 Å / Isotropic thermal model : mixed / 交差検証法 : THROUGHOUT / σ(F) : 0 / 位相誤差 : 21.8 / 立体化学のターゲット値 : TWIN_LSQ_FRfactor 反射数 %反射 Selection details Rfree 0.206 1890 5.04 % random Rwork 0.176 - - - all 0.177 37508 - - obs 0.177 37508 97.08 % -
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL原子変位パラメータ Biso mean : 27.8 Å2 精密化ステップ サイクル : LAST / 解像度 : 1.8515→28.329 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3458 0 23 164 3645
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.009 3591 X-RAY DIFFRACTION f_angle_d1.218 4853 X-RAY DIFFRACTION f_dihedral_angle_d16.43 1372 X-RAY DIFFRACTION f_chiral_restr0.056 586 X-RAY DIFFRACTION f_plane_restr0.006 626
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection obs % reflection obs (%)1.8515-1.9015 0.2275 128 0.2086 2376 2504 79 1.9015-1.9573 0.2184 151 0.2042 2686 2837 91 1.9573-2.0204 0.2576 137 0.2057 2828 2965 95 2.0204-2.0925 0.2384 163 0.2059 2792 2955 94 2.0925-2.1762 0.2051 138 0.1956 2795 2933 94 2.1762-2.275 0.2272 142 0.1937 2761 2903 94 2.275-2.3946 0.2236 134 0.1904 2781 2915 94 2.3946-2.5442 0.248 146 0.1967 2795 2941 93 2.5442-2.74 0.2827 154 0.2065 2730 2884 93 2.74-3.0144 0.2033 155 0.1967 2777 2932 94 3.0144-3.4476 0.1803 143 0.1742 2809 2952 94 3.4476-4.3323 0.1646 144 0.1319 2723 2867 93 4.3323-17.3204 0.1811 137 0.1419 2734 2871 92
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 17) 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 1.9634 -0.2331 0.8036 0.8808 0.2016 1.4613 0.1029 -0.0576 -0.1308 -0.0629 0.0261 0.2252 -0.0717 -0.369 -0.1236 0.0907 0.0271 -0.0054 0.1824 0.0119 0.1391 16.0073 14.4634 31.5077 2 2.637 0.3264 0.003 3.8389 -1.5639 7.1154 0.0615 -0.2288 0.0043 -0.0302 -0.0632 -0.0422 -0.1286 -0.0528 0.0392 0.156 0.0416 0.0104 0.1584 -0.0147 0.0575 26.8083 17.8271 44.101 3 1.1235 0.8147 -0.8087 3.1394 -0.3322 3.1789 -0.0608 -0.5833 -0.2439 0.5246 -0.2381 0.0978 -0.0492 -0.0463 0.2281 0.1933 0.0396 0.0472 0.3356 0.0646 0.1686 15.9717 14.2471 48.8752 4 1.9352 0.43 0.3896 0.5844 0.0273 1.0393 0.0153 -0.5202 -0.1748 0.2206 0.0913 0.3148 -0.1113 -0.6537 -0.0126 0.1702 0.0919 0.066 0.4514 0.0618 0.2556 9.6788 15.5107 48.5553 5 2.0325 0.786 0.4091 1.197 -0.4486 0.4944 0.0212 -0.5332 -0.1032 0.3098 0.0789 0.4681 -0.0317 -0.2969 -0.0432 0.1465 0.0753 0.0563 0.5931 0.125 0.4518 -1.3181 13.5716 43.1078 6 0.8601 0.1891 0.1417 0.2241 0.1454 0.3752 -0.0815 -0.1895 -0.0288 0.0612 0.0794 0.2274 0.0452 -0.236 0.047 0.0942 0.0097 -0.0245 0.4733 0.1162 0.4377 -2.0678 12.1164 35.4157 7 1.5519 -1.9888 0.3513 3.6953 -1.5233 1.0837 0.1941 0.1635 -0.4257 -0.1182 0.0841 0.0727 0.5524 -0.3834 -0.2722 0.236 -0.0285 -0.1156 0.2535 -0.0279 0.415 10.2048 4.1144 22.884 8 2.9467 -0.1725 -3.6656 0.3299 0.1918 4.5607 0.1058 0.324 0.0371 -0.1386 0.0011 0.4103 -0.3464 -0.4605 -0.0921 0.1602 0.0305 -0.0733 0.5085 0.05 0.3396 -1.5132 13.9272 23.7785 9 1.3192 -0.5303 0.3842 1.2143 -0.6137 1.3548 0.1008 0.0027 -0.1962 -0.0265 -0.0348 0.0044 0.3281 0.3564 -0.0807 0.1426 0.0617 -0.0202 0.1846 0.0053 0.13 4.5905 54.7692 36.1999 10 2.2588 0.0215 2.0773 0.8019 -0.3621 3.5338 -0.0095 0.1504 -0.001 -0.0267 -0.0232 0.0043 -0.0206 0.3324 0.0458 0.0987 0.0159 0.0185 0.1773 0.0077 0.0795 2.3906 65.8586 24.283 11 1.6712 0.4984 -0.2369 1.929 0.6777 2.0935 0.0823 0.2178 -0.2166 -0.5653 -0.0829 0.192 -0.0442 0.1662 -0.0429 0.3193 0.1579 -0.067 0.2494 -0.1083 0.1982 3.4623 53.6108 18.0758 12 0.8463 0.2545 0.044 1.1 -0.3351 0.5345 0.0946 0.341 -0.3552 -0.3489 0.0315 -0.1819 0.4918 0.5521 -0.1152 0.368 0.1946 -0.0364 0.3698 -0.0904 0.1785 8.5996 52.1537 17.345 13 1.7798 -1.1939 0.047 2.2928 0.0314 0.9878 0.1709 0.1154 -0.2728 -0.1455 0.0184 0.1984 0.2826 0.1503 0.1132 0.3128 0.2379 -0.0746 0.2908 -0.1008 0.2739 9.117 45.8989 22.617 14 0.0045 -0.0544 -0.027 0.8929 0.0742 0.2836 0.0119 0.2405 -0.4438 -0.1539 0.01 -0.1837 0.2561 0.1683 0.029 0.4385 0.2208 -0.0675 0.3328 -0.1352 0.4816 13.8894 40.1491 21.0637 15 0.9624 -0.9155 -0.4493 0.8802 0.4803 0.4907 -0.1097 -0.0633 -0.3271 0.1223 0.0718 0.1466 0.1549 0.0723 0.1087 0.5002 0.2635 -0.1184 0.2646 -0.0898 0.5621 10.5566 33.7121 32.8502 16 1.5284 -0.0949 -0.2764 2.1413 0.2664 1.2572 0.0415 -0.077 -0.4101 0.2134 -0.0261 -0.02 0.3129 0.1269 -0.0278 0.3142 0.099 -0.0866 0.188 0.0082 0.3125 5.9677 41.9903 37.4147 17 3.0688 -1.0437 -1.3384 1.9341 -0.0086 2.4217 -0.0816 -0.4398 -0.4751 0.3869 0.2087 -0.0486 0.4884 0.2746 -0.1041 0.4392 0.1043 -0.0861 0.2662 0.053 0.271 7.529 41.5985 44.3407
精密化 TLSグループ 大きな表を表示 (4 x 17) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 66 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 67 through 82 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 83 through 100 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 101 through 156 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 157 through 183 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 184 through 202 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 203 through 213 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 214 through 225 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 1 through 66 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 67 through 83 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 84 through 100 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 101 through 137 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 138 through 154 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 155 through 176 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 177 through 191 )16 X-RAY DIFFRACTION 16 chain 'B'