ソフトウェア 名称 バージョン 分類 PHENIX(1.18.2_3874: ???)精密化 HKL-3000データ削減 HKL-3000データスケーリング PHASER位相決定
精密化 構造決定の手法 : 分子置換 / 解像度 : 2→33.65 Å / SU ML : 0.19 / 交差検証法 : THROUGHOUT / σ(F) : 1.36 / 位相誤差 : 21.68 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Rfree 0.215 2000 5.51 % Rwork 0.1804 - - obs 0.1824 36275 99.55 %
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精密化ステップ サイクル : LAST / 解像度 : 2→33.65 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3645 0 6 267 3918
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.01 3733 X-RAY DIFFRACTION f_angle_d1.39 5088 X-RAY DIFFRACTION f_dihedral_angle_d14.454 534 X-RAY DIFFRACTION f_chiral_restr0.067 642 X-RAY DIFFRACTION f_plane_restr0.011 660
LS精密化 シェル 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2-2.05 0.2723 136 0.1986 2325 X-RAY DIFFRACTION 97 2.05-2.1 0.2523 142 0.1969 2433 X-RAY DIFFRACTION 100 2.1-2.17 0.2273 140 0.1835 2404 X-RAY DIFFRACTION 100 2.17-2.24 0.2083 141 0.1743 2408 X-RAY DIFFRACTION 100 2.24-2.32 0.2003 141 0.179 2428 X-RAY DIFFRACTION 100 2.32-2.41 0.2583 142 0.1818 2430 X-RAY DIFFRACTION 100 2.41-2.52 0.238 143 0.192 2451 X-RAY DIFFRACTION 100 2.52-2.65 0.2783 142 0.1944 2430 X-RAY DIFFRACTION 100 2.65-2.82 0.2306 142 0.2027 2447 X-RAY DIFFRACTION 100 2.82-3.03 0.2612 143 0.2033 2442 X-RAY DIFFRACTION 100 3.03-3.34 0.2124 144 0.1885 2467 X-RAY DIFFRACTION 100 3.34-3.82 0.1905 144 0.1787 2474 X-RAY DIFFRACTION 100 3.82-4.81 0.1919 146 0.1526 2500 X-RAY DIFFRACTION 99 4.81-33.65 0.1828 154 0.1721 2636 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 33) 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 3.5537 2.7263 -1.5533 6.5623 -2.4399 4.3159 0.0759 0.0874 0.3544 0.0005 0.2169 0.4931 -0.314 -0.2353 -0.3559 0.2178 -0.022 0.0231 0.3175 -0.0237 0.2488 -4.4075 -11.7376 -14.9598 2 2.2491 1.2324 -0.5724 4.3024 -1.1805 2.5943 -0.0757 0.1724 0.2091 -0.3813 0.2438 0.4847 0.0032 -0.2435 -0.1407 0.1932 0.0443 -0.0095 0.2383 -0.0115 0.2045 1.4573 -6.1436 -15.5395 3 9.2393 4.4943 -4.6442 4.5553 -4.7002 4.8185 0.2879 -0.3183 0.1976 0.3145 -0.2263 1.1116 -0.6719 -0.8978 -0.2026 0.384 0.0625 0.0192 0.3408 -0.0777 0.3227 -4.3728 -4.9754 -7.4482 4 6.4743 1.4767 -1.9135 6.2445 -2.1604 2.5836 0.0455 -0.3658 -0.1363 0.1797 0.1479 0.1254 -0.2844 -0.838 -0.1917 0.1957 -0.0064 -0.0389 0.2847 0.0326 0.279 0.4784 -14.6102 -7.335 5 5.1777 5.2799 -1.8206 5.5216 -2.5559 4.0809 -0.4319 0.5849 -0.0922 -0.1911 0.4984 -0.5463 0.0839 0.1114 -0.0043 0.272 0.0256 -0.0114 0.2008 -0.0006 0.2126 8.1443 -5.9917 -19.9438 6 6.0417 1.1333 -2.4468 5.4115 -2.1329 1.5484 0.5552 -1.1915 0.1382 1.0355 -0.5223 0.1114 -0.5694 0.324 -0.0894 0.3103 -0.0874 -0.0084 0.3298 -0.0657 0.2432 6.6999 -4.0736 -4.3659 7 2.8022 1.0226 -0.7095 4.2467 1.251 9.0255 0.4426 -0.5328 -0.1184 0.4318 -0.0334 -0.2945 -0.519 0.0649 -0.1563 0.242 -0.0577 -0.0232 0.3268 0.0203 0.2513 4.5328 -14.1867 -1.325 8 3.6226 -0.4066 -1.1823 3.2186 0.1569 5.2009 -0.1007 -0.3258 0.0777 0.2824 -0.1144 -0.0937 -0.029 0.3948 0.135 0.2031 0.0002 0.004 0.2128 0.024 0.2441 16.2716 -10.2076 -12.7624 9 4.4364 3.1629 3.7553 4.2321 6.0613 8.9968 -0.0563 -0.7347 -0.4773 0.2387 -0.1598 -0.2337 0.3749 0.2336 -0.0031 0.2113 -0.0379 -0.0095 0.4486 0.0358 0.4202 10.8635 -16.2178 -7.6934 10 7.2414 -6.4293 -2.6148 7.6914 4.4138 3.1939 -0.9329 -1.3165 -1.4939 1.093 0.4049 -0.4132 1.0014 0.5765 0.244 0.3544 0.0051 0.0578 0.3462 0.1542 0.5917 4.8265 -23.8089 -7.5046 11 3.1931 -0.8587 -1.0898 3.8444 0.0233 4.538 -0.1274 -0.1384 0.0023 -0.0186 0.1105 -0.1267 0.0654 0.2113 -0.0232 0.1385 -0.0069 -0.0343 0.2087 -0.0007 0.1711 16.3461 5.1853 -30.2017 12 2.028 -1.6236 -0.1923 2.7568 1.6044 3.0667 0.0734 -0.1111 0.0736 0.2948 -0.0778 -0.2452 0.1069 -0.0489 0.0247 0.1952 -0.0284 0.0033 0.222 0.021 0.1936 15.3408 3.482 -20.058 13 7.319 -3.3538 -4.0027 3.569 3.3663 8.3006 0.2324 0.241 0.1754 -0.229 -0.0198 -0.3352 -0.1642 0.4583 -0.1836 0.2443 -0.0196 -0.0234 0.2038 0.0184 0.2011 20.5265 11.4582 -25.994 14 2.1985 -0.7206 0.4627 5.1243 -0.2426 2.2308 0.1912 -0.1592 -0.0229 -0.1105 -0.1438 -0.2802 -0.0464 0.1581 -0.0952 0.245 -0.0323 -0.0122 0.2656 0.0185 0.1877 21.6524 9.6 -12.5189 15 7.3355 -0.9375 -1.2836 2.4007 2.7268 6.2973 -0.206 -0.3618 0.7069 0.5526 0.2983 -0.6207 -0.0731 -0.0218 -0.1347 0.1993 -0.0559 -0.0348 0.2734 0.0052 0.2045 21.4888 17.2193 -18.6751 16 4.5899 1.7552 2.6202 6.6301 5.117 4.319 0.1124 -0.0061 -0.5162 0.212 0.538 -1.1987 -0.5864 0.5006 -0.8986 0.5013 0.041 0.0338 0.5545 -0.0463 0.5355 26.2767 -6.6001 -42.4169 17 4.1318 -0.2474 -0.1516 1.8849 -0.9967 3.2918 0.1797 -0.1522 -0.5551 0.2897 -0.1088 -0.2249 0.5603 -0.1204 -0.0694 0.2958 0.031 -0.0062 0.2207 -0.0144 0.2313 18.5156 -16.9088 -54.6354 18 3.5137 0.1662 -0.8677 9.8721 1.9768 1.9888 0.174 0.4984 -0.3503 -0.3734 -0.036 -0.6335 0.2654 0.5875 -0.1494 0.3307 0.1196 -0.0027 0.3396 -0.0062 0.3038 23.7166 -13.7026 -61.56 19 3.301 -1.381 -0.3318 5.9112 1.8291 3.6803 -0.0478 0.0552 -0.4084 0.2293 0.0665 -0.1237 0.4844 -0.007 -0.1067 0.2168 -0.0068 -0.0167 0.1726 0.014 0.239 14.1149 -15.2628 -56.7248 20 6.4535 1.4594 2.056 7.3662 4.4217 2.9476 0.1096 0.7826 -0.1099 -1.0369 0.0011 -0.0253 -0.3065 0.4739 -0.0452 0.339 0.0099 -0.034 0.2464 0.0382 0.2096 14.5054 -7.0624 -64.0564 21 1.7422 -0.7364 0.0465 2.5921 0.6547 2.8452 -0.0656 0.3596 -0.201 -0.0897 -0.2129 0.2714 0.297 -0.169 0.2116 0.2435 -0.0548 -0.0394 0.211 -0.0157 0.2056 9.1289 -14.9651 -60.7832 22 7.0945 -2.535 0.4833 8.0481 4.4922 3.181 -0.1961 -0.0871 -0.2114 -0.3356 -0.0347 0.5432 -0.1519 -0.8713 0.0491 0.2337 -0.0221 -0.0131 0.2763 -0.0235 0.273 2.6905 -6.1209 -58.3155 23 5.691 -0.1951 0.0851 2.3244 -3.354 9.0997 0.0628 0.6146 -0.9338 0.0238 0.0325 0.869 0.8364 -0.8371 -0.0847 0.3946 -0.1161 -0.0172 0.3405 -0.0823 0.4624 5.7733 -20.9866 -60.8275 24 3.342 -3.2355 -1.6823 3.6111 0.8224 9.325 0.2602 0.572 1.531 -0.344 -0.0317 1.0313 -0.5629 -1.0249 0.0961 0.4344 0.1866 -0.0495 0.4739 -0.0214 0.6085 3.6414 15.9687 -33.4173 25 7.5433 -2.7343 -3.9703 6.9081 2.438 2.3583 -0.1753 -0.1189 0.3958 0.1705 0.4048 -0.6429 0.1063 0.5117 -0.2889 0.1635 -0.0166 -0.0587 0.2621 -0.0207 0.2049 18.9214 10.9999 -39.3427 26 3.0449 1.1372 0.7658 3.7396 0.0869 3.6743 0.0319 0.0207 -0.1846 0.0385 -0.0667 0.109 0.3641 -0.3128 0.054 0.2043 -0.0009 -0.0216 0.1795 -0.0223 0.1583 11.3564 1.5502 -39.9415 27 9.3619 7.7802 -1.6094 7.7503 -1.6324 1.9273 -0.2165 0.1949 0.0781 -0.3314 0.1748 0.0014 0.1591 0.067 0.0325 0.1721 0.0358 -0.0032 0.1716 -0.0292 0.1937 14.1536 5.5188 -48.6283 28 3.1824 2.7151 -2.8413 3.8543 -1.207 3.8872 0.328 -0.3583 0.6832 0.3912 0.0256 0.3668 -0.1341 -0.4393 -0.3355 0.2578 -0.0082 -0.0108 0.4036 0.0127 0.2526 6.5015 12.6077 -39.4511 29 2.884 4.0782 -4.0505 7.3833 -4.1139 7.0769 0.2258 -0.0625 0.7314 0.2445 0.1943 0.4913 -0.0596 -0.1699 -0.3525 0.1607 0.0128 -0.0154 0.2025 -0.0243 0.1717 9.6687 13.7424 -44.9 30 4.0211 4.9147 2.5188 6.7612 3.4115 1.9683 -0.2464 0.448 0.1945 -0.5136 0.2187 0.309 -0.0988 0.2521 -0.0255 0.2954 0.0296 0.0033 0.3593 0.0209 0.2059 16.1451 15.203 -59.1336 31 2.2592 0.0966 1.0584 3.528 1.5949 4.0671 0.2587 0.1681 0.014 -0.3933 -0.2613 0.3872 0.2675 -0.5853 0.0345 0.2911 0.0254 -0.0536 0.3025 0.0141 0.243 6.5442 10.276 -55.1995 32 2.6565 -0.7907 -2.5645 5.2092 2.6389 3.1744 0.3218 0.7072 1.1749 -0.4471 -0.0322 0.1512 -0.705 0.3464 -0.2298 0.3441 0.0283 0.0025 0.309 0.0236 0.4313 22.6743 25.6039 -53.228 33 8.1556 4.7273 -2.9366 7.2499 -2.8523 5.0384 0.2991 -0.3794 0.3194 0.1604 -0.2006 0.6029 0.3472 -0.1932 -0.0583 0.1986 -0.0306 0.0042 0.2737 -0.0171 0.1918 5.5624 12.3323 -47.3327
精密化 TLSグループ 大きな表を表示 (4 x 33) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 3 through 16 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 17 through 30 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 31 through 44 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 45 through 54 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 55 through 60 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 61 through 74 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 75 through 83 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 84 through 100 )9 X-RAY DIFFRACTION 9 chain 'A' and (resid 101 through 107 )10 X-RAY DIFFRACTION 10 chain 'A' and (resid 108 through 117 )11 X-RAY DIFFRACTION 11 chain 'C' and (resid 12 through 46 )12 X-RAY DIFFRACTION 12 chain 'C' and (resid 47 through 67 )13 X-RAY DIFFRACTION 13 chain 'C' and (resid 68 through 93 )14 X-RAY DIFFRACTION 14 chain 'C' and (resid 94 through 120 )15 X-RAY DIFFRACTION 15 chain 'C' and (resid 121 through 140 )16 X-RAY DIFFRACTION 16 chain 'B' and (resid -1 through 7 ) 17 X-RAY DIFFRACTION 17 chain 'B'