ソフトウェア 名称 バージョン 分類 PHENIXdev_5533精密化 Aimlessデータスケーリング XDSデータ削減 PHASER位相決定
精密化 構造決定の手法 : 分子置換 / 解像度 : 2.65→48.96 Å / SU ML : 0.38 / 交差検証法 : FREE R-VALUE / σ(F) : 1.33 / 位相誤差 : 27.07 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Rfree 0.2628 2728 5.01 % Rwork 0.2077 - - obs 0.2104 54470 99.97 %
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.1 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL精密化ステップ サイクル : LAST / 解像度 : 2.65→48.96 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 12432 0 158 28 12618
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.003 12830 X-RAY DIFFRACTION f_angle_d0.512 17455 X-RAY DIFFRACTION f_dihedral_angle_d13.638 4634 X-RAY DIFFRACTION f_chiral_restr0.041 2053 X-RAY DIFFRACTION f_plane_restr0.004 2235
LS精密化 シェル 大きな表を表示 (7 x 19) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.65-2.7 0.3533 149 0.308 2668 X-RAY DIFFRACTION 100 2.7-2.75 0.3809 126 0.2891 2655 X-RAY DIFFRACTION 100 2.75-2.81 0.3494 145 0.2714 2700 X-RAY DIFFRACTION 100 2.81-2.87 0.3387 136 0.2625 2632 X-RAY DIFFRACTION 100 2.87-2.93 0.3309 152 0.262 2660 X-RAY DIFFRACTION 100 2.93-3.01 0.3253 149 0.2604 2682 X-RAY DIFFRACTION 100 3.01-3.09 0.3204 162 0.2828 2666 X-RAY DIFFRACTION 100 3.09-3.18 0.3825 157 0.296 2628 X-RAY DIFFRACTION 100 3.18-3.28 0.3327 131 0.2871 2705 X-RAY DIFFRACTION 100 3.28-3.4 0.3313 130 0.2379 2708 X-RAY DIFFRACTION 100 3.4-3.54 0.2832 128 0.2102 2713 X-RAY DIFFRACTION 100 3.54-3.7 0.279 147 0.2151 2695 X-RAY DIFFRACTION 100 3.7-3.89 0.2944 133 0.2119 2728 X-RAY DIFFRACTION 100 3.89-4.13 0.2456 147 0.177 2747 X-RAY DIFFRACTION 100 4.13-4.45 0.2252 156 0.1668 2705 X-RAY DIFFRACTION 100 4.45-4.9 0.2071 133 0.1644 2777 X-RAY DIFFRACTION 100 4.9-5.61 0.2343 129 0.195 2810 X-RAY DIFFRACTION 100 5.61-7.06 0.2826 164 0.2217 2812 X-RAY DIFFRACTION 100 7.07-48.96 0.2136 154 0.1862 3051 X-RAY DIFFRACTION 100
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 25) 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 1.7411 -1.1242 0.1995 3.1062 -0.8752 2.1466 -0.0508 -0.0826 0.1767 -0.4317 0.2943 0.2958 0.8443 -0.0046 -0.1354 0.9377 -0.1554 -0.1174 0.6385 -0.0078 0.6211 28.0549 -25.1095 -40.3198 2 0.5878 -0.0766 0.272 2.433 0.4049 3.3319 -0.3897 0.4664 -0.0241 0.1926 0.5327 1.2521 1.0877 -1.1138 -0.2485 1.1167 -0.3909 -0.053 0.9389 0.16 1.0631 17.9073 -31.8806 -33.3374 3 2.0167 -0.8394 -1.6164 8.098 0.0772 2.4057 -0.6475 0.1325 0.025 0.2222 0.4713 0.1343 0.3009 -0.2526 0.0634 0.9544 -0.1111 0.063 0.703 0.0201 0.7313 28.0665 -25.8269 -23.8036 4 1.9522 0.0195 -0.7034 2.5666 1.1674 2.602 -0.091 0.1504 0.0272 0.0214 0.1089 0.1306 0.0769 -0.3615 -0.0109 0.523 0.0888 0.0281 0.6354 0.0669 0.5676 22.3179 -0.6447 -14.9671 5 0.2994 -1.1599 -0.8855 4.0002 2.3386 3.2852 -0.2435 -0.1412 -0.3103 0.5569 0.0508 0.4495 0.9496 -0.0178 0.2366 0.9329 -0.0135 -0.042 0.6123 0.0108 0.8852 32.2097 -25.8028 -19.4064 6 3.3305 -0.8002 -1.1752 2.5265 2.0068 3.7562 -0.2367 -0.6058 0.5094 0.7968 0.2116 -0.3775 0.1628 -0.0425 0.0562 0.781 0.2082 0.0257 0.6119 0.0314 0.5854 24.4149 4.4268 4.6218 7 2.9841 -2.3362 -0.0318 2.4745 0.8647 3.7815 0.1693 0.4001 0.1271 -0.4898 0.0307 0.0763 0.3692 0.1534 -0.2011 0.713 -0.0286 -0.07 0.7733 0.049 0.5451 42.09 -7.7219 -62.9134 8 3.6212 0.1458 1.6896 2.4709 0.3749 3.7909 -0.1685 0.7409 0.1905 -0.4878 0.1638 -0.6605 -0.6503 0.1693 0.1408 0.9363 -0.0855 0.069 0.928 0.2506 0.8186 46.4679 5.9364 -58.9774 9 1.4749 0.5415 -0.2183 1.2627 -0.0529 2.0163 -0.0878 -0.1262 0.0907 -0.0926 0.0887 -0.2145 -0.0297 0.4797 -0.0225 0.4948 -0.0542 0.019 0.8377 -0.0569 0.7867 65.6522 5.5439 -38.0554 10 1.7606 -0.3972 -0.53 1.4396 0.2917 3.29 0.0077 -0.0185 0.4888 -0.2817 0.0652 -0.1042 -0.1537 -0.2063 0.018 0.4991 -0.009 0.0286 0.5536 0.0273 0.598 51.6523 4.8845 -48.9798 11 1.9426 0.047 -0.3432 1.129 -0.6 1.6881 -0.1496 -0.2158 -0.0105 -0.1709 0.0324 -0.0744 -0.4961 -0.1297 -0.0145 0.6411 -0.1524 0.1005 0.6945 -0.0004 0.7406 62.3709 19.3335 -40.2346 12 1.4435 0.6526 0.0867 0.9494 1.3062 3.5515 0.164 -0.4304 0.8537 -0.2295 -0.0687 -0.0469 -0.6434 0.5215 -0.1274 0.7806 -0.3041 -0.0773 1.0006 -0.0079 1.0924 77.6004 19.3449 -29.2228 13 2.2117 0.291 0.4255 0.6142 -0.8039 1.6271 0.0611 0.2555 0.0373 0.2298 -0.0415 0.0696 -0.2877 0.1099 -0.0579 0.6723 0.1586 -0.1055 0.6741 -0.0816 0.5738 54.2434 2.8377 -5.0474 14 1.6241 0.7101 0.7401 0.4019 -0.0742 2.9611 -0.1248 -0.1892 -0.2473 0.3312 0.1392 -0.5008 0.6363 0.8624 -0.097 0.8893 0.2785 -0.1532 1.2197 -0.1274 0.9251 64.0024 -3.8741 -2.7942 15 2.554 -0.1656 0.0273 2.232 1.5376 3.5047 -0.1676 -0.1037 0.1978 0.0994 0.1179 -0.3188 0.3233 0.4634 -0.0153 1.0628 0.2899 -0.1025 0.8088 0.0343 0.795 55.1857 -13.9186 -7.5646 16 2.0399 0.1479 -1.8671 2.5098 0.6628 2.8237 -0.1626 -0.2016 0.0351 0.247 0.1647 -0.0192 0.3482 0.3022 -0.0427 0.5755 0.1507 -0.0537 0.593 -0.0736 0.5002 55.8457 -20.6195 -36.2778 17 2.096 -1.8635 -0.0209 2.573 0.1939 0.8591 -0.0874 -0.1739 0.4146 -0.0441 0.1349 -0.3904 0.0464 0.4333 -0.078 0.6008 0.1441 0.0072 0.8548 -0.0695 0.5997 66.2658 -16.4361 -35.9798 18 1.0877 1.3313 0.8264 1.7519 0.2721 6.3549 0.2426 -0.3313 -0.4865 0.355 0.4554 -0.162 1.0364 0.6542 -0.6278 0.8852 0.2824 -0.0933 0.8445 -0.0454 0.5733 48.2566 -13.6436 -4.0617 19 2.5077 0.3145 -0.1822 1.2892 -1.1598 1.1727 -0.663 -0.233 -0.3667 -0.4085 0.3058 0.1453 1.2299 0.0188 0.0064 0.9177 0.3723 -0.0201 0.737 0.0052 0.5958 53.7129 -30.8265 -29.1726 20 0.6862 -0.3849 1.5481 2.1249 0.1737 4.0012 -0.2039 0.3999 -0.1033 -0.3572 -0.1711 -0.0475 0.0818 0.1805 0.3646 1.0639 0.2248 0.0658 0.7789 -0.1079 0.6614 60.2723 -36.5289 -46.8433 21 2.0303 0.3381 0.2476 1.6326 0.5311 2.4689 -0.1859 0.2264 0.1683 0.2557 0.1146 0.3393 -0.5157 -0.0946 0.017 0.8349 0.0184 0.0398 0.5458 -0.0092 0.9032 43.0082 25.88 -17.937 22 3.614 0.8126 0.7628 1.4898 1.4253 1.9054 -0.0236 0.0697 1.1904 0.1058 0.3235 0.5302 -0.935 -0.3306 -0.2322 1.2753 0.1404 0.1992 0.7412 0.2601 1.2233 38.9013 29.8296 -28.7673 23 2.6845 0.5444 0.4386 1.2526 0.3534 1.6837 0.0808 0.1033 0.2733 0.0166 0.1154 0.0367 -0.2773 -0.4454 -0.1695 0.5506 0.1031 0.0017 0.809 0.138 0.6655 23.5108 8.7794 -36.8796 24 2.4244 1.1943 1.8312 1.3122 0.7751 1.968 -0.5232 0.5388 0.7586 -0.891 0.3929 0.49 -0.7065 -0.0252 0.2501 0.6137 0.1953 0.0258 0.6686 0.1936 0.87 30.4395 22.3873 -44.8074 25 3.499 -1.574 0.4951 2.6497 0.3807 3.3396 0.0778 1.3781 0.1874 -0.8014 -0.1136 0.6157 0.1253 -1.409 0.0403 0.6281 0.0875 -0.1005 1.5068 0.2399 0.8765 9.2258 1.9511 -54.8354
精密化 TLSグループ 大きな表を表示 (4 x 25) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 5 through 85 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 86 through 123 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 124 through 155 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 156 through 316 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 317 through 384 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 385 through 426 )7 X-RAY DIFFRACTION 7 chain 'B' and (resid 4 through 126 )8 X-RAY DIFFRACTION 8 chain 'B' and (resid 127 through 155 )9 X-RAY DIFFRACTION 9 chain 'B' and (resid 156 through 281 )10 X-RAY DIFFRACTION 10 chain 'B' and (resid 282 through 363 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 364 through 395 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 396 through 426 )13 X-RAY DIFFRACTION 13 chain 'C' and (resid 4 through 73 )14 X-RAY DIFFRACTION 14 chain 'C' and (resid 74 through 126 )15 X-RAY DIFFRACTION 15 chain 'C' and (resid 127 through 155 )16 X-RAY DIFFRACTION 16 chain 'C'