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 : 1.98→49.28 Å / SU ML : 0.23 / 交差検証法 : THROUGHOUT / σ(F) : 1.91 / 位相誤差 : 23.04 Rfactor 反射数 %反射 Rfree 0.2131 6711 4.99 % Rwork 0.1761 - - obs 0.178 72838 99.86 %
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 : 107.92 Å2 / Biso mean : 46.9353 Å2 / Biso min : 20.85 Å2 精密化ステップ サイクル : final / 解像度 : 1.98→49.28 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 8236 0 56 258 8550 Biso mean - - 55.99 48.31 - 残基数 - - - - 1020
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID 数 Refine-ID Rms タイプ 1 1 A4885 X-RAY DIFFRACTION 8.434 TORSIONAL1 2 B4885 X-RAY DIFFRACTION 8.434 TORSIONAL1 3 C4885 X-RAY DIFFRACTION 8.434 TORSIONAL1 4 D4885 X-RAY DIFFRACTION 8.434 TORSIONAL
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 (%)1.98-2 0.3331 205 0.3005 4055 4260 97 2-2.03 0.3022 253 0.282 4319 4572 100 2.03-2.05 0.3247 216 0.2714 4184 4400 100 2.05-2.08 0.2855 235 0.2798 4322 4557 100 2.08-2.1 0.3236 233 0.261 4191 4424 100 2.1-2.13 0.2939 236 0.2501 4327 4563 100 2.13-2.16 0.2807 219 0.2345 4238 4457 100 2.16-2.2 0.2927 214 0.2354 4295 4509 100 2.2-2.23 0.2553 237 0.2263 4276 4513 100 2.23-2.27 0.2965 210 0.2231 4237 4447 100 2.27-2.31 0.2401 216 0.2158 4294 4510 100 2.31-2.35 0.2144 215 0.2135 4292 4507 100 2.35-2.39 0.2366 219 0.2074 4218 4437 100 2.39-2.44 0.2673 221 0.2066 4304 4525 100 2.44-2.49 0.2741 245 0.2043 4261 4506 100 2.49-2.55 0.2841 219 0.1972 4267 4486 100 2.55-2.62 0.2808 222 0.2007 4244 4466 100 2.62-2.69 0.1958 196 0.1805 4295 4491 100 2.69-2.77 0.2341 191 0.182 4276 4467 100 2.77-2.86 0.2414 226 0.1812 4315 4541 100 2.86-2.96 0.1982 227 0.1878 4256 4483 100 2.96-3.08 0.23 188 0.1847 4310 4498 100 3.08-3.22 0.1999 211 0.1904 4294 4505 100 3.22-3.39 0.2294 250 0.174 4223 4473 100 3.39-3.6 0.1677 230 0.1564 4279 4509 100 3.6-3.88 0.1747 266 0.1444 4198 4464 100 3.88-4.26 0.1984 241 0.1385 4257 4498 100 4.27-4.88 0.1712 231 0.1251 4272 4503 100 4.88-6.15 0.1716 213 0.1531 4281 4494 100 6.15-49.28 0.1851 226 0.1604 4269 4495 100
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 32) 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 1.1434 1.3335 1.8276 2.5436 1.8851 2.2143 0.0337 -0.1363 -0.0084 -0.1949 0.1046 -0.3121 0.2002 0.5455 -0.1804 0.2502 0.0897 0.0071 0.3068 0.0498 0.3056 -35.1209 33.7418 -11.7352 2 8.8748 -5.7791 7.0367 2.0957 -9.6923 9.8257 0.5599 0.6476 -0.4032 -0.9154 -0.0432 0.2906 1.061 -0.0937 -0.4782 0.5631 0.0007 -0.0755 0.3879 -0.059 0.3912 -43.7634 22.4596 -27.385 3 1.6198 0.2405 -0.3185 1.3015 0.3374 4.1657 0.0933 0.0118 0.0864 0.0262 -0.1128 -0.1199 0.1851 0.1257 0.0196 0.1779 0.0374 -0.003 0.2105 0.0677 0.2565 -31.5255 26.8527 -7.4674 4 4.5313 0.3143 2.4242 4.3701 -1.1938 7.564 0.3098 -0.3898 -0.5248 0.2785 -0.1206 0.1083 0.6376 -0.2157 -0.208 0.2991 0.0133 0.0369 0.2006 0.0236 0.278 -34.9354 17.4788 -4.0227 5 9.1395 2.4576 -1.5328 8.8293 -3.4235 4.8764 0.2368 -0.7237 -0.9189 0.406 -0.5368 -1.0809 0.4176 1.1375 0.3084 0.4242 0.0337 -0.0785 0.6514 0.0649 0.4425 -21.9084 28.0317 10.5452 6 5.8697 4.947 3.3772 2.2394 8.9389 9.2358 0.0415 -0.6712 0.0007 1.3329 -0.1666 0.5787 1.1102 -0.1157 0.0557 0.6058 0.0051 0.0128 0.378 0.1303 0.3862 -33.5529 16.8737 13.3493 7 6.8558 -0.8901 0.7316 3.4944 0.2289 5.7484 -0.118 -0.3205 -0.4973 0.1365 -0.0794 -0.0722 0.7713 0.0961 0.1811 0.4506 0.0491 -0.0219 0.2208 0.1216 0.3462 -28.2596 10.6727 -0.3425 8 6.2886 2.7558 0.0675 5.0988 -1.2164 4.0572 0.1093 -0.2578 -0.5824 0.2982 -0.1716 -0.3279 0.8604 0.4279 0.0908 0.5039 0.1429 -0.0258 0.3067 0.0963 0.4091 -23.5865 7.1917 1.939 9 6.768 5.4409 3.9304 6.6233 3.5422 7.9118 0.3963 0.0608 -0.7155 0.3452 -0.1819 -0.3232 0.8399 0.2544 -0.2205 0.4266 0.1546 0.014 0.2865 0.0439 0.3515 -25.006 13.6686 -12.7454 10 1.5668 1.0216 -0.2891 5.6556 -2.2255 5.8842 -0.0524 0.2807 0.1232 -0.4097 0.0508 -0.3263 -0.3999 0.3429 0.0001 0.2098 0.0223 0.043 0.3848 0.0242 0.3488 -16.5705 49.0926 -15.1461 11 1.9948 -0.3888 0.4514 1.4892 -0.3991 5.9995 0.1169 0.0064 0.0635 0.0228 -0.0619 -0.0222 -0.4845 0.1995 -0.0668 0.1885 -0.0235 0.0168 0.2199 -0.0099 0.2609 -23.5974 51.9711 -4.2099 12 2.8704 2.3017 0.3136 7.1099 -0.0746 4.2055 0.2703 -0.5315 0.0921 0.3118 -0.2379 0.5969 -0.2469 -0.5061 -0.044 0.3259 0.007 -0.0025 0.4552 -0.0298 0.3278 -31.0325 53.7538 6.2881 13 2.4711 3.0043 0.8532 7.828 2.8551 7.5755 0.3668 -0.4076 0.0611 0.6212 -0.3593 0.1093 -0.2887 -0.0313 -0.0235 0.2977 -0.019 0.0177 0.4196 -0.0469 0.2942 -26.3634 53.7205 16.474 14 5.7287 0.2336 2.0777 4.7764 1.3139 8.4012 -0.0015 -0.4704 0.6886 0.339 -0.0414 0.0121 -1.6053 -0.3158 0.0892 0.7118 0.0389 0.0777 0.3088 -0.029 0.4209 -31.1345 66.0101 6.9544 15 2.2018 3.3283 5.0989 9.6861 2.5477 8.1568 -0.3107 -0.2502 0.8804 -0.3277 -0.1134 0.4267 -1.8415 -0.45 0.5907 0.7717 0.1157 0.1048 0.4726 -0.1141 0.5407 -33.8268 67.776 1.9886 16 6.9666 0.461 -2.8275 8.8973 -2.4806 6.0211 0.4521 0.0553 0.9403 0.0558 -0.2888 -0.1024 -1.2499 -0.0484 -0.2055 0.5569 0.0543 -0.0268 0.3128 0.004 0.3498 -30.7672 63.6993 -9.0471 17 0.6251 0.5021 -1.1678 2.4185 -0.0194 4.3771 0.0602 -0.0726 -0.1237 0.2333 0.0936 -0.1442 0.0069 0.8072 -0.1634 0.2131 0.0422 0.0051 0.4446 0.0024 0.3159 -13.2688 43.499 -17.2886 18 1.0329 0.4219 -0.4953 2.0758 0.3204 1.9014 -0.0279 0.2227 0.0484 -0.0462 0.0635 -0.0421 0.0034 0.4757 -0.0444 0.1911 0.0745 0.0387 0.5625 0.0415 0.3171 -13.2271 37.1757 -27.6587 19 4.7037 1.4794 0.4187 4.0277 -0.2602 2.8749 0.037 0.5852 -0.0112 -0.2774 0.0511 -0.0804 -0.1166 0.2952 -0.1125 0.2604 0.1545 0.0441 0.7559 -0.0006 0.3305 -6.5707 33.0465 -36.5634 20 9.5618 -0.0869 -2.0925 1.1833 -0.1257 2.9988 -0.1368 1.3994 0.0891 -0.3776 0.1267 0.1983 0.232 0.1665 0.0474 0.4867 0.0986 -0.0011 0.8375 -0.0179 0.3943 -14.0266 32.8088 -48.1532 21 4.6169 0.568 -2.203 1.815 0.4197 4.0054 -0.0766 0.2269 -0.1657 -0.1055 0.0784 -0.2467 0.3425 0.5915 0.0316 0.3122 0.2103 0.0269 0.6499 -0.0046 0.3761 -4.6329 23.0059 -34.1972 22 2.2059 1.4891 0.7776 1.2685 -0.3974 2.1643 0.1952 -0.0076 0.0157 -0.1224 -0.0134 -0.272 -0.2226 0.3118 -0.155 0.2643 0.1077 0.0107 0.3375 0.0871 0.318 -35.2249 36.2987 -24.777 23 0.1389 0.9832 -1.0825 5.6519 -5.0712 6.3186 -0.0037 -0.0296 0.0492 0.101 0.1204 0.2297 -0.026 -0.3241 -0.1287 0.212 0.0847 -0.0283 0.3835 -0.0065 0.2713 -45.1211 39.2871 -19.2195 24 2.1252 1.6661 0.9734 3.6049 0.975 2.3644 -0.0477 0.0568 0.2094 0.0897 -0.108 0.1375 -0.3907 -0.3812 0.1394 0.328 0.1391 -0.045 0.4504 0.071 0.3478 -40.7015 48.9016 -19.1304 25 0.5132 -0.4288 0.8345 2.6989 -0.8897 3.2607 0.0211 0.2926 0.0144 -0.1639 -0.0427 0.0048 -0.1398 -0.2307 0.0206 0.1998 0.1004 -0.0329 0.4374 0.0464 0.3235 -42.0235 40.7335 -34.3833 26 8.3621 2.5177 -1.5453 5.4178 2.8357 2.515 0.0382 0.0385 0.0693 -0.4204 -0.0854 -0.0589 -0.2123 -0.3141 0.042 0.2931 0.1716 -0.0723 0.3718 0.1042 0.3358 -47.8294 49.1397 -36.2281 27 7.183 1.6674 6.1867 7.3548 2.6335 6.2572 -0.5574 0.8652 0.7109 -0.6102 0.4691 0.1834 -1.0406 0.5605 0.0613 0.5462 0.0182 0.0206 0.7332 0.1228 0.4874 -29.5209 52.3641 -44.9948 28 2.1294 2.0504 -2.5244 6.5107 -1.3789 7.0743 -0.0385 1.163 -0.0921 -0.5404 -0.2093 -0.4082 -0.0229 0.5846 0.2982 0.5125 0.2004 -0.0784 0.6875 0.0371 0.3835 -44.3427 48.8958 -50.6608 29 2.2889 1.2132 0.1706 4.8327 0.2156 3.4988 0.018 0.0698 0.0113 -0.2588 -0.0694 0.1614 -0.4186 -0.3241 0.0712 0.3871 0.1804 -0.0845 0.4454 0.1129 0.3513 -49.2262 55.2674 -36.9205 30 2.0661 9.4348 5.7206 8.9437 6.0243 6.5311 -0.2565 0.4904 0.3248 -0.3901 0.1585 0.2259 -0.849 -0.3312 0.1744 0.639 0.3033 0.0002 0.6063 0.118 0.4727 -50.163 61.3427 -43.259 31 6.3126 -0.5783 5.6423 0.2422 -0.547 5.5325 -0.316 -0.0624 0.4134 -0.0105 0.0312 0.2607 -1.4171 -0.505 0.4189 0.5622 0.2947 -0.0438 0.5956 0.0492 0.4489 -48.6042 61.294 -33.3747 32 6.0048 1.107 -0.6554 5.9004 -0.4526 4.9061 -0.0978 0.3588 0.6638 0.1418 0.2598 0.7757 -0.7407 -0.9426 -0.1845 0.412 0.2185 -0.0524 0.4528 0.0703 0.3504 -47.0321 55.3539 -23.9113
精密化 TLSグループ 大きな表を表示 (6 x 32) 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 24 ) A-1 - 24 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 25 through 40 )A25 - 40 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 41 through 105 )A41 - 105 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 106 through 149 )A106 - 149 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 150 through 167 )A150 - 167 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 168 through 189 )A168 - 189 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 190 through 207 )A190 - 207 8 X-RAY DIFFRACTION 8 chain 'A' and (resid 208 through 235 )A208 - 235 9 X-RAY DIFFRACTION 9 chain 'A' and (resid 236 through 253 )A236 - 253 10 X-RAY DIFFRACTION 10 chain 'B' and (resid -1 through 40 ) B-1 - 40 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 41 through 133 )B41 - 133 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 134 through 162 )B134 - 162 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 163 through 189 )B163 - 189 14 X-RAY DIFFRACTION 14 chain 'B' and (resid 190 through 220 )B190 - 220 15 X-RAY DIFFRACTION 15 chain 'B' and (resid