ソフトウェア 名称 バージョン 分類 XDSデータ削減 Aimless0.7.4データスケーリング PHASER2.8.3位相決定 PHENIXdev-3699 精密化 PDB_EXTRACT3.25 データ抽出
精密化 構造決定の手法 : 分子置換開始モデル : 6VH9解像度 : 1.94→49.24 Å / SU ML : 0.19 / 交差検証法 : THROUGHOUT / σ(F) : 1.91 / 位相誤差 : 21.19 Rfactor 反射数 %反射 Rfree 0.2086 6997 4.88 % Rwork 0.1681 - - obs 0.1701 77403 99.93 %
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 : 99.45 Å2 / Biso mean : 37.8561 Å2 / Biso min : 15.44 Å2 精密化ステップ サイクル : final / 解像度 : 1.94→49.24 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 8236 0 70 499 8805 Biso mean - - 48.28 40.88 - 残基数 - - - - 1020
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0 / Total num. of bins used : 30
大きな表を表示 (7 x 30) 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 (%)1.94-1.96 0.332 186 0.2717 4456 4642 99 1.96-1.98 0.2672 194 0.2557 4606 4800 100 1.98-2.01 0.2903 223 0.2369 4527 4750 100 2.01-2.03 0.318 226 0.2394 4576 4802 100 2.03-2.06 0.2799 222 0.2285 4518 4740 100 2.06-2.09 0.2567 232 0.2232 4551 4783 100 2.09-2.12 0.297 216 0.2014 4621 4837 100 2.12-2.15 0.2296 251 0.1985 4480 4731 100 2.15-2.18 0.2799 216 0.2021 4608 4824 100 2.18-2.22 0.2507 214 0.187 4562 4776 100 2.22-2.26 0.2338 204 0.1839 4555 4759 100 2.26-2.3 0.2229 251 0.1802 4532 4783 100 2.3-2.34 0.2412 233 0.1785 4556 4789 100 2.34-2.39 0.2131 233 0.1755 4502 4735 100 2.39-2.44 0.2508 249 0.1788 4525 4774 100 2.44-2.5 0.2345 243 0.1727 4599 4842 100 2.5-2.56 0.2075 249 0.1785 4556 4805 100 2.56-2.63 0.2253 232 0.1738 4487 4719 100 2.63-2.71 0.2135 264 0.1753 4541 4805 100 2.71-2.8 0.2349 259 0.1788 4502 4761 100 2.8-2.9 0.2123 274 0.1775 4517 4791 100 2.9-3.01 0.2416 193 0.1783 4574 4767 100 3.01-3.15 0.245 256 0.1779 4519 4775 100 3.15-3.31 0.1937 234 0.1686 4531 4765 100 3.31-3.52 0.1929 234 0.1566 4560 4794 100 3.52-3.79 0.1827 207 0.1463 4596 4803 100 3.79-4.17 0.1886 240 0.1382 4537 4777 100 4.18-4.78 0.1393 267 0.1184 4476 4743 100 4.78-6.02 0.1658 265 0.1463 4521 4786 100 6.02-49.24 0.1995 230 0.1626 4549 4779 100
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 29) 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 1.2358 0.1278 0.2841 1.6523 0.2165 3.3321 0.0739 0.0247 -0.0639 -0.0492 -0.096 0.0674 0.3642 -0.0309 0.0226 0.1425 0.0195 -0.0015 0.1609 0.0227 0.1915 -34.2697 25.8529 -10.1819 2 0.377 0.7166 -0.2346 6.2743 1.254 2.8889 0.1677 -0.3762 -0.1644 1.0385 -0.1305 -0.1928 0.6519 0.3434 -0.0423 0.4187 0.0276 -0.0279 0.3648 0.0798 0.2426 -28.9385 20.2389 8.3522 3 2.8903 0.8176 0.1687 4.3754 -2.3009 4.9899 0.1437 -0.1075 -0.4169 0.14 -0.2056 -0.1818 0.8483 0.2957 0.0554 0.4363 0.1007 -0.016 0.2045 0.0262 0.3006 -24.982 9.9793 -2.9588 4 4.6242 3.6044 -3.6388 4.4384 -1.0026 4.8776 -0.0206 0.2301 -0.0115 -0.2431 0.396 0.2554 -0.0029 -0.191 -0.3744 0.0875 0.0213 0.0105 0.2305 -0.0119 0.1926 -20.5056 43.4729 -10.1604 5 8.3922 -5.1764 -6.9722 7.4511 4.7796 8.0021 0.3427 0.648 0.9735 -0.9078 0.3763 -0.7956 -1.154 0.9873 -0.7634 0.4966 -0.2277 0.0605 0.5759 0.0305 0.3945 -10.2399 57.0384 -22.6715 6 2.1609 -0.321 1.1089 1.6481 -1.0471 5.0482 0.0678 0.0009 0.0472 0.0335 -0.0829 -0.0819 -0.3111 0.3108 0.0258 0.1264 -0.0135 0.012 0.1654 -0.0212 0.1826 -24.554 49.598 -5.2929 7 2.8468 -0.1173 -1.4416 3.1294 0.8563 4.9883 0.1144 -0.0811 0.2464 0.0879 0.0015 -0.2111 -0.7877 0.5074 -0.1145 0.2608 -0.0809 -0.0327 0.2149 0.0118 0.2143 -21.6715 58.234 -0.0552 8 4.3958 2.3735 2.81 5.8543 7.1687 8.8497 -0.2037 -0.6955 0.4745 0.1313 -0.3284 0.7795 -0.2211 -1.0683 0.5392 0.2993 -0.0279 0.0127 0.5189 -0.0552 0.3112 -35.8788 45.6259 11.1616 9 4.6488 6.839 -0.7876 2.147 -2.4457 2.1414 0.3819 -0.5526 -0.1459 0.9931 -0.3846 -0.5646 -0.4385 0.4921 -0.0012 0.4186 -0.0409 0.015 0.3321 -0.0454 0.3298 -24.8432 55.9384 16.8753 10 2.0553 0.4551 4.2228 4.8615 -1.2161 5.6546 -0.4102 -0.2406 0.6214 0.1611 0.1001 0.0162 -1.1184 0.2001 0.3291 0.5386 -0.0079 0.0354 0.2801 -0.0796 0.2334 -28.7443 64.3539 3.939 11 9.174 6.7665 5.9141 8.6623 1.4782 6.1156 -0.1191 -1.1909 1.2554 0.9265 -0.2565 0.6832 -1.0748 -0.8729 0.3674 0.6869 0.1629 0.0386 0.3709 -0.0992 0.4654 -33.25 67.6477 10.9202 12 9.782 5.2444 7.2766 7.331 3.2162 8.7786 -0.6697 -0.3134 1.2127 -0.54 -0.085 0.5549 -1.6564 -0.4214 0.7694 0.5351 0.1133 0.007 0.2986 -0.0527 0.4179 -34.3202 67.2347 1.1743 13 8.6823 4.031 -2.5033 2.0652 -1.7758 10.0053 -0.0343 0.0622 1.0901 -0.1368 -0.0943 0.2417 -1.3073 0.1676 0.097 0.4618 0.0356 -0.0609 0.1695 0.0226 0.3774 -30.5453 63.3459 -9.0463 14 1.6055 0.0724 -0.0478 1.2384 0.3708 1.674 0.0004 -0.0266 -0.0627 0.1624 0.1226 -0.1494 -0.0774 0.812 -0.1326 0.1622 0.0413 0.0105 0.5171 0.0124 0.2696 -14.0561 41.0618 -20.0668 15 8.4179 1.2247 -0.3612 6.942 -1.04 0.2953 -0.048 -0.4235 -0.3083 0.2195 -0.0064 -0.2086 0.2154 0.5539 0.0576 0.2148 0.148 0.0498 0.4553 -0.0008 0.1844 -14.1309 29.7058 -19.253 16 2.6323 -0.842 -0.2191 1.2723 0.0602 0.6139 0.0163 0.3303 0.095 -0.1143 0.082 -0.1717 -0.0527 0.7586 -0.1147 0.1645 0.0222 0.0256 0.6301 0.0168 0.2626 -9.9461 38.3823 -33.272 17 9.3959 1.9766 -8.8312 7.8278 -1.0839 8.4088 -0.7064 0.6483 -1.3096 -0.8128 -0.0821 -0.5044 0.932 0.4004 0.6985 0.3308 0.093 0.0262 0.5715 -0.0733 0.3865 -21.7567 29.2826 -46.6961 18 7.0943 -0.4183 -0.7825 2.6493 0.3661 3.4477 0.0566 1.0722 0.5161 -0.5671 0.0009 0.199 -0.1735 0.0907 -0.0918 0.2778 0.0913 0.1356 1.1115 0.01 0.2314 -6.7225 34.6997 -49.6388 19 6.1207 2.1649 0.7535 4.5366 -0.8711 1.1947 -0.0356 0.1288 -0.2715 -0.4525 -0.0072 -0.4878 0.316 0.7339 0.0007 0.2979 0.1774 0.0807 0.7574 -0.1125 0.2654 -4.4267 25.4997 -37.1271 20 6.7129 0.003 -1.773 1.6036 -0.2797 0.9154 0.3297 0.1859 -0.664 -0.2401 -0.0409 0.1015 0.713 0.5699 -0.0425 0.2921 0.3549 0.0503 0.8773 -0.1419 0.3172 -3.1617 20.2277 -39.3667 21 9.6566 2.5352 0.8848 5.8296 1.0953 3.7636 -0.0183 -0.1166 -0.6614 0.1313 0.1265 -0.6273 0.4318 0.8206 -0.1041 0.3157 0.2674 0.0373 0.7015 -0.0271 0.3022 -7.5366 23.8467 -24.3922 22 -0.0467 0.0814 0.2459 1.7169 -1.2433 2.6738 0.0975 0.0728 -0.012 0.1217 0.0064 0.1164 -0.0506 -0.2969 -0.1121 0.129 0.0524 -0.0159 0.294 0.0086 0.2568 -40.3157 37.7517 -21.7033 23 1.7688 1.4892 1.5724 3.956 1.3444 3.696 -0.003 -0.007 0.0823 0.1371 -0.1951 0.278 -0.3443 -0.3816 0.1948 0.192 0.0874 -0.0357 0.2446 0.0351 0.2569 -40.3835 48.672 -19.0777 24 1.7704 -0.4716 0.1872 1.4207 0.0905 1.6302 0.0213 0.1774 0.0408 -0.1181 -0.0377 0.1953 -0.2187 -0.3915 0.0123 0.1611 0.0926 -0.0324 0.315 0.0057 0.2155 -42.9873 42.2003 -34.6122 25 9.2416 0.6146 6.7795 8.7063 1.1549 5.0673 -0.5727 1.0701 1.0889 -0.8702 0.1243 0.3244 -1.5838 0.3648 0.4427 0.5391 0.0047 -0.0139 0.5811 0.1331 0.3291 -29.5159 52.0118 -45.0028 26 2.0349 2.0069 -5.3339 4.7123 -1.4353 5.0891 -0.0025 1.0668 -0.2189 -0.3568 -0.1159 -0.0471 -0.3468 -0.1505 0.1144 0.3705 0.1602 -0.0872 0.5319 -0.0211 0.2695 -44.2658 48.5968 -50.4214 27 5.4172 2.0758 2.787 7.0612 2.1381 5.4912 -0.0166 0.0495 0.2159 -0.7335 -0.285 0.2849 -0.7129 -0.4127 0.3103 0.3853 0.2214 -0.0601 0.3677 0.0834 0.2697 -49.1277 55.0589 -36.9284 28 9.4077 -0.7879 5.6088 1.0873 -1.5215 4.4695 0.0057 0.252 0.6766 -0.3044 -0.2864 -0.0091 -1.0465 -0.1838 0.3513 0.6509 0.3114 -0.0527 0.3882 0.0572 0.3801 -49.3387 61.0848 -38.4719 29 9.7116 1.6948 -0.0698 7.3213 -0.4947 5.2617 -0.1649 0.1733 0.7985 0.2632 0.0275 0.7764 -0.8209 -0.6392 0.0651 0.3749 0.1737 -0.0586 0.3106 0.0155 0.2609 -46.735 55.0773 -23.8369
精密化 TLSグループ 大きな表を表示 (6 x 29) 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 133 ) A-1 - 133 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 134 through 189 )A134 - 189 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 190 through 253 )A190 - 253 4 X-RAY DIFFRACTION 4 chain 'B' and (resid -1 through 24 ) B-1 - 24 5 X-RAY DIFFRACTION 5 chain 'B' and (resid 25 through 40 )B25 - 40 6 X-RAY DIFFRACTION 6 chain 'B' and (resid 41 through 105 )B41 - 105 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 106 through 149 )B106 - 149 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 150 through 167 )B150 - 167 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 168 through 189 )B168 - 189 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 190 through 207 )B190 - 207 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 208 through 221 )B208 - 221 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 222 through 235 )B222 - 235 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 236 through 253 )B236 - 253 14 X-RAY DIFFRACTION 14 chain 'C' and (resid -1 through 53 ) C-1 - 53 15 X-RAY DIFFRACTION 15 chain 'C' and (resid 54 through 74 )C54 - 74 16 X-RAY DIFFRACTION 16 chain 'C'