ソフトウェア 名称 バージョン 分類 PHASER位相決定 REFMAC5.6.0117精密化 SCALAデータスケーリング
精密化 構造決定の手法 : 分子置換 / 解像度 : 2.4→46.22 Å / Cor.coef. Fo :Fc : 0.943 / Cor.coef. Fo :Fc free : 0.902 / SU B : 12.634 / SU ML : 0.155 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.339 / ESU R Free : 0.237 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN USED IFRfactor 反射数 %反射 Selection details Rfree 0.228 2557 5.1 % RANDOM Rwork 0.175 - - - obs 0.177 50334 - -
溶媒の処理 イオンプローブ半径 : 0.8 Å / 減衰半径 : 0.8 Å / VDWプローブ半径 : 1.2 Å / 溶媒モデル : MASK原子変位パラメータ Biso mean : 25.8 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.39 Å2 -0.2 Å2 0 Å2 2- - -0.39 Å2 0 Å2 3- - - 0.59 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.4→46.22 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 8048 0 0 431 8479
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.009 0.019 8293 X-RAY DIFFRACTION r_angle_refined_deg1.259 1.95 11225 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.801 5 1023 X-RAY DIFFRACTION r_dihedral_angle_2_deg35.531 23.594 384 X-RAY DIFFRACTION r_dihedral_angle_3_deg14.016 15 1452 X-RAY DIFFRACTION r_dihedral_angle_4_deg14.922 15 52 X-RAY DIFFRACTION r_chiral_restr0.092 0.2 1238 X-RAY DIFFRACTION r_gen_planes_refined0.005 0.021 6244
LS精密化 シェル 解像度 : 2.4→2.46 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.293 197 - Rwork 0.213 3513 - obs - - 99.2 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 36) 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 0.2718 0.0877 -0.2281 3.1348 -1.2351 0.8246 -0.0753 0.0153 -0.0453 -0.0291 0.0544 -0.0159 0.0017 0.0091 0.0208 0.1333 -0.0327 0.0227 0.1449 -0.0276 0.1514 49.46 6.7938 108.6116 2 0.412 -0.6158 0.3592 2.7329 -0.0168 0.4895 -0.0539 -0.0065 0.0164 -0.1089 0.0636 -0.129 -0.0364 -0.0075 -0.0097 0.1558 -0.0466 0.0554 0.1765 -0.0106 0.1512 46.944 4.0612 105.2148 3 3.5674 1.6817 1.0303 2.3976 -1.1015 1.8763 -0.0992 0.1405 -0.0867 -0.1223 0.0068 -0.1093 0.0519 0.097 0.0924 0.1309 0.0224 0.0743 0.1522 -0.0645 0.1781 66.9654 -1.4514 104.15 4 0.6628 -0.476 0.3112 0.7682 -0.1879 0.2062 -0.0889 -0.0542 0.0524 -0.0883 0.0076 -0.1166 -0.0354 0.034 0.0812 0.1384 -0.0065 0.0439 0.1717 -0.0086 0.18 55.6358 8.5592 113.6801 5 1.2913 -0.5726 0.8955 0.9379 -0.4091 0.8196 -0.094 0.049 -0.0525 -0.06 0.0191 -0.0901 0.0118 -0.0013 0.0749 0.1313 -0.015 0.0606 0.1569 -0.0269 0.1361 56.9301 3.4977 104.1171 6 1.5694 1.2278 0.1524 7.7622 2.2803 0.7034 0.1041 0.1619 0.178 -0.3574 -0.1258 0.1561 -0.1173 -0.0824 0.0217 0.1972 -0.0545 -0.018 0.1706 0.0562 0.1236 37.4797 19.4918 100.7026 7 0.1373 -0.2404 0.337 2.2507 -0.8974 1.1353 -0.0653 0.0249 -0.0034 0.0056 -0.0174 0.0202 0.0347 -0.0313 0.0827 0.1641 -0.0382 0.0449 0.1456 -0.0366 0.1516 34.4537 -1.7448 112.1645 8 0.3096 -0.308 -0.2861 0.8859 0.2103 0.2983 -0.086 0.0574 -0.0709 -0.098 -0.056 -0.0668 0.0656 -0.0571 0.1421 0.2066 -0.0642 0.0001 0.1359 -0.0649 0.1871 32.3284 -3.7317 98.4266 9 9.3672 4.7678 1.2133 7.3623 2.1084 1.9607 -0.195 -0.1349 0.1535 0.1115 -0.2154 0.2899 0.0685 -0.2239 0.4104 0.1315 -0.0588 0.0234 0.201 -0.0834 0.0973 18.5025 -2.1375 96.8912 10 0.8927 0.3848 -0.4694 1.8587 -3.1152 5.2996 -0.079 0.1016 -0.0631 -0.152 0.0162 -0.0022 0.2663 -0.0548 0.0628 0.2411 -0.0804 0.0513 0.1027 -0.0791 0.1477 32.9047 -6.3538 111.19 11 0.9451 -0.541 0.1506 2.488 -1.1547 2.2038 -0.0567 0.0424 0.0049 -0.1595 0.1456 0.1556 0.1203 -0.2402 -0.0889 0.139 -0.0745 -0.0114 0.1616 -0.015 0.1724 20.1974 6.4176 111.683 12 0.874 0.0614 0.7032 1.1345 0.2946 1.9578 -0.0432 0.0361 -0.1876 -0.0987 0.0089 0.0111 0.2167 0.0372 0.0342 0.1774 -0.0483 0.0618 0.0671 -0.0266 0.1354 37.2031 -10.6444 110.0829 13 0.5992 0.2385 0.1658 0.727 0.3661 1.4631 0.0159 -0.047 0.0289 -0.0629 0.0881 -0.0191 0.0347 -0.0415 -0.104 0.1536 -0.0239 0.0092 0.1327 0.0061 0.1656 24.4591 20.2511 125.2221 14 2.9027 0.5656 -0.6731 0.9239 0.5251 3.4885 0.1545 -0.1487 0.3509 -0.0307 0.1703 0.0913 -0.2296 -0.0505 -0.3248 0.1138 0.0392 0.0362 0.1127 0.0494 0.1999 17.2251 30.987 130.7367 15 13.9181 -1.1312 -1.5051 8.7187 1.4061 0.3543 0.2361 0.2276 -0.4529 -0.1564 -0.3122 0.4778 -0.0494 -0.0709 0.0761 0.1129 0.0006 -0.0195 0.1743 0.0574 0.1675 3.8446 22.1933 140.3991 16 1.0352 -0.1134 -1.0636 0.6895 0.1489 1.2279 0.0029 0.0423 0.0785 -0.0307 0.0373 0.0802 -0.0779 -0.1464 -0.0401 0.1079 0.0063 -0.001 0.1419 0.0141 0.1826 17.2274 23.1155 129.9743 17 0.1666 0.0937 -0.0623 0.6688 -0.6544 1.5637 -0.0303 -0.0068 0.0359 0.0676 0.0873 0.0765 0.0356 -0.1577 -0.0571 0.0991 -0.0086 0.0166 0.1734 0.0016 0.177 18.0965 18.5267 132.2571 18 0.8735 3.2591 0.4558 14.4893 3.2859 1.3337 -0.1096 0.1448 0.0792 -0.5796 -0.0904 0.4823 -0.2092 -0.3228 0.2 0.1024 -0.0199 -0.0572 0.2454 0.0127 0.1296 23.7071 19.7113 106.4774 19 2.9501 -0.8296 -1.7675 0.4064 0.757 1.4529 0.0199 -0.1397 0.0337 -0.0114 0.009 -0.0104 -0.0217 0.062 -0.0288 0.1376 -0.0144 -0.014 0.1671 0.0267 0.1469 52.1722 9.6547 137.3319 20 1.0158 0.5407 -0.7641 0.9393 -0.2324 0.6354 0.0285 -0.1821 -0.1004 0.1252 -0.1211 -0.0737 0.0452 0.1027 0.0926 0.1055 -0.0077 -0.0343 0.213 0.0134 0.1566 54.5778 9.7793 145.9725 21 7.5161 -5.0265 10.2015 9.5809 -5.4799 15.3722 -0.2783 1.2917 1.2086 0.7383 -0.819 -2.0175 0.0605 1.3665 1.0973 0.1408 -0.1807 -0.1591 0.5129 0.1556 0.5648 65.4046 25.0843 149.3892 22 0.4147 0.3744 -0.3306 1.3572 0.9832 1.9242 -0.0138 -0.1495 -0.0033 0.0762 -0.039 -0.0358 0.1182 0.2439 0.0528 0.0819 -0.0001 -0.0326 0.2139 0.0014 0.1629 55.8938 13.7255 142.3456 23 0.2893 -0.2022 0.0083 1.166 0.0461 0.4322 -0.013 -0.1194 0.0819 0.0035 0.048 -0.0465 -0.0729 0.1783 -0.035 0.1023 -0.0215 -0.0109 0.2054 -0.0316 0.1621 55.0046 18.9929 139.5978 24 1.4138 1.0199 -0.1755 0.8779 -0.356 4.1574 -0.1934 -0.0296 -0.1963 -0.0587 0.0299 -0.0638 0.26 0.062 0.1635 0.1262 0.0675 0.0535 0.0973 0.0286 0.2047 56.337 -5.4538 130.3993 25 1.9929 -0.9176 -1.1426 1.0142 0.2427 0.8305 -0.0471 -0.084 -0.0811 -0.0165 -0.0299 -0.0302 0.0911 0.0202 0.077 0.1406 -0.0131 0.0029 0.1369 -0.0059 0.1593 37.4804 -0.2243 139.1279 26 0.9769 0.4973 0.361 0.9344 0.4549 0.2591 0.0131 -0.1533 -0.0228 0.129 -0.0251 -0.0841 0.0404 -0.0085 0.012 0.1742 -0.0186 0.0345 0.1588 0.0438 0.1538 40.3174 -4.2633 144.4917 27 5.1803 2.8234 -0.7704 1.5525 -0.5866 2.5429 -0.0314 -0.1822 -0.102 -0.0248 -0.0869 -0.0828 0.0884 -0.1308 0.1183 0.1817 0.0202 0.0231 0.0954 0.0244 0.1951 34.2037 -20.7657 142.4226 28 3.0851 -1.172 -0.081 2.0153 0.1566 0.3178 -0.1245 -0.1685 -0.036 0.138 0.0453 0.027 0.1049 -0.0512 0.0791 0.158 -0.0101 0.0339 0.1455 0.0359 0.1185 34.513 -0.7849 142.5046 29 0.3865 0.3652 0.2896 0.5974 0.0087 0.7926 -0.0839 -0.0398 -0.0239 -0.0482 0.0158 0.0167 0.1016 -0.0629 0.0681 0.185 -0.0093 0.0596 0.1238 -0.0012 0.1611 33.5284 -8.9897 135.6639 30 3.3678 -1.8892 1.7316 1.3979 -0.9546 1.842 -0.0349 -0.3069 -0.0105 0.1405 0.1179 0.1475 -0.0998 0.0871 -0.083 0.1344 -0.0248 0.0364 0.1993 -0.0326 0.1148 34.4866 13.331 149.0672 31 0.5588 -0.1092 0.6397 0.1716 0.322 2.4501 0.0225 0.0157 -0.0163 -0.0994 0.0133 -0.0396 -0.0851 0.0157 -0.0358 0.156 -0.0316 0.0248 0.122 0.001 0.1765 37.3933 30.1009 121.2617 32 0.7831 0.3969 -0.2178 0.2111 -0.0794 0.1861 0.018 0.0193 0.1162 0.0026 0.0377 0.0574 -0.0284 0.0295 -0.0557 0.1709 -0.013 0.0281 0.1254 -0.0252 0.1787 34.852 35.982 119.2698 33 4.6654 0.3549 0.3203 9.7978 -1.9348 6.7679 0.1003 -0.3696 0.0329 0.1583 -0.1667 -0.2917 -0.3052 0.1288 0.0664 0.1236 -0.0654 0.0393 0.0949 -0.0165 0.1875 47.1359 46.2504 107.5037 34 0.4519 -0.0239 -0.1165 0.3842 -0.7591 1.6344 -0.0656 -0.0364 0.1171 0.0236 0.0553 -0.069 -0.1185 -0.0916 0.0103 0.1843 -0.0191 0.025 0.0911 -0.0116 0.1992 39.387 35.4005 117.8289 35 0.5135 -0.2977 -0.1288 1.3938 0.1793 0.439 0.0251 0.013 0.0458 0.0288 -0.0151 -0.0931 -0.0132 0.0986 -0.0099 0.1484 -0.0486 0.0253 0.1296 -0.0161 0.1737 45.5413 30.4934 112.3245 36 1.3038 -0.7168 -0.2432 1.1803 -0.7997 1.2408 -0.0602 -0.1695 0.1088 0.1762 0.1564 0.0128 -0.1732 -0.1234 -0.0962 0.1613 -0.0373 0.0139 0.1304 -0.0582 0.183 34.7955 34.6465 134.3555
精密化 TLSグループ 大きな表を表示 (5 x 36) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A2 - 29 2 X-RAY DIFFRACTION 2 A30 - 47 3 X-RAY DIFFRACTION 3 A48 - 75 4 X-RAY DIFFRACTION 4 A76 - 122 5 X-RAY DIFFRACTION 5 A123 - 157 6 X-RAY DIFFRACTION 6 A158 - 170 7 X-RAY DIFFRACTION 7 B2 - 35 8 X-RAY DIFFRACTION 8 B36 - 55 9 X-RAY DIFFRACTION 9 B56 - 77 10 X-RAY DIFFRACTION 10 B78 - 95 11 X-RAY DIFFRACTION 11 B96 - 131 12 X-RAY DIFFRACTION 12 B132 - 170 13 X-RAY DIFFRACTION 13 C5 - 35 14 X-RAY DIFFRACTION 14 C36 - 55 15 X-RAY DIFFRACTION 15 C56 - 66 16 X-RAY DIFFRACTION 16 C67 - 95 17 X-RAY DIFFRACTION 17 C96 - 157 18 X-RAY DIFFRACTION 18 C158 - 170 19 X-RAY DIFFRACTION 19 D2 - 30 20 X-RAY DIFFRACTION 20 D31 - 56 21 X-RAY DIFFRACTION 21 D57 - 66 22 X-RAY DIFFRACTION 22 D67 - 96 23 X-RAY DIFFRACTION 23 D97 - 154 24 X-RAY DIFFRACTION 24 D155 - 170 25 X-RAY DIFFRACTION 25 E3 - 29 26 X-RAY DIFFRACTION 26 E30 - 55 27 X-RAY DIFFRACTION 27 E56 - 75 28 X-RAY DIFFRACTION 28 E76 - 96 29 X-RAY DIFFRACTION 29 E97 - 152 30 X-RAY DIFFRACTION 30 E153 - 170 31 X-RAY DIFFRACTION 31 F3 - 28 32 X-RAY DIFFRACTION 32 F29 - 56 33 X-RAY DIFFRACTION 33 F57 - 66 34 X-RAY DIFFRACTION 34 F67 - 96 35 X-RAY DIFFRACTION 35 F97 - 146 36 X-RAY DIFFRACTION 36 F147 - 170