ソフトウェア 名称 バージョン 分類 HKL-2000データ収集 PHASER位相決定 REFMAC5.6.0117精密化 DENZOデータ削減 SCALEPACKデータスケーリング
精密化 構造決定の手法 : 分子置換開始モデル : PDB ENTRY 4D9I解像度 : 2.19→40.65 Å / Cor.coef. Fo :Fc : 0.95 / Cor.coef. Fo :Fc free : 0.923 / SU B : 14.508 / SU ML : 0.197 / 交差検証法 : THROUGHOUT / ESU R : 0.351 / ESU R Free : 0.242 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUTRfactor 反射数 %反射 Selection details Rfree 0.26065 3590 5 % RANDOM Rwork 0.21338 - - - obs 0.21574 67710 98.03 % -
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 : 42.953 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.06 Å2 0 Å2 -0.04 Å2 2- - -0.01 Å2 0 Å2 3- - - -0.08 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.19→40.65 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 11015 0 35 503 11553
拘束条件 大きな表を表示 (5 x 33) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.005 0.02 11280 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.022 1.948 15332 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg4.853 5 1444 X-RAY DIFFRACTION r_dihedral_angle_2_deg33.904 24.949 489 X-RAY DIFFRACTION r_dihedral_angle_3_deg13.879 15 1769 X-RAY DIFFRACTION r_dihedral_angle_4_deg10.318 15 43 X-RAY DIFFRACTION r_chiral_restr0.06 0.2 1731 X-RAY DIFFRACTION r_gen_planes_refined0.003 0.021 8535 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refinedX-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refinedX-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refinedX-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refinedX-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refinedX-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_itX-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_itX-RAY DIFFRACTION r_scbond_itX-RAY DIFFRACTION r_scangle_itX-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
LS精密化 シェル 解像度 : 2.191→2.248 Å / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.382 237 - Rwork 0.35 4709 - obs - - 93.78 %
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 1.4461 -0.2424 0.0698 0.5188 -0.0846 0.5829 0.0351 -0.0246 0.0595 -0.0298 -0.0267 -0.1529 0.0553 0.1283 -0.0085 0.1351 -0.0093 -0.0123 0.0769 0.0111 0.1406 20.023 -3.185 44.823 2 1.6975 0.3817 -0.2755 1.2918 -0.1637 0.0616 0.0048 -0.0479 0.2671 0.0591 0.0463 -0.0501 0.0053 -0.022 -0.0511 0.2096 -0.0126 -0.0172 0.1135 0.0001 0.1343 10.465 4.655 44.795 3 2.4769 1.8 0.9661 2.8296 1.3935 1.6803 -0.0612 0.3924 0.2836 -0.1882 0.1484 -0.2878 -0.1461 0.0756 -0.0872 0.1437 -0.0153 0.0226 0.0836 0.0697 0.2746 24.989 17.331 31.631 4 9.731 -0.296 -0.5903 0.0712 0.44 3.4134 0.0703 1.2162 0.4229 -0.0493 -0.0727 -0.0347 -0.1942 -0.1347 0.0024 0.1839 0.0486 0.0477 0.2842 0.1919 0.1751 14.052 9.54 22.737 5 6.4622 0.199 0.4503 3.8719 0.1764 1.9393 -0.022 1.4371 -0.0205 -0.3337 -0.0973 -0.4595 0.175 0.4719 0.1193 0.108 0.0662 0.1006 0.4452 0.0754 0.1108 23.835 3.984 20.21 6 1.6808 0.1191 -0.6032 0.7825 -0.7795 1.0132 0.0275 -0.045 0.0535 0.0211 -0.0445 -0.1265 0.0217 0.0372 0.017 0.2056 -0.0112 -0.028 0.1081 0.0077 0.1084 19.994 -1.208 46.501 7 1.4236 -0.1312 0.2946 0.509 -0.0335 0.2471 0.0297 0.1005 -0.1597 0.0005 -0.008 -0.1288 0.0364 -0.0675 -0.0218 0.2427 -0.0036 -0.0087 0.095 -0.0114 0.1162 8.348 -10.484 42.893 8 1.6775 -0.3699 0.4613 0.4431 -0.4552 0.7807 -0.0045 0.1095 -0.0004 -0.0404 -0.0506 -0.081 0.0295 -0.0553 0.0552 0.2273 -0.0011 -0.0009 0.1332 -0.0217 0.056 2.082 -5.172 38.375 9 1.8907 -0.0044 0.7157 0.2606 -0.4385 1.2607 -0.071 0.1941 0.2361 -0.0532 0.1045 0.1379 0.0245 -0.3008 -0.0335 0.1391 0.0152 -0.0385 0.2159 -0.0033 0.1595 -34.72 2.778 35.06 10 0.8333 0.283 -1.0261 0.427 -0.4031 1.5781 0.1056 -0.0038 0.1872 0.0597 -0.0389 0.0865 -0.0774 -0.033 -0.0667 0.2213 0.0057 -0.0014 0.1356 -0.0185 0.1538 -26.376 4.295 46.141 11 3.1385 -4.4229 -4.1514 16.5439 0.694 8.0738 -0.1204 -0.0715 -0.0013 1.1383 0.1818 0.0914 -0.3108 0.0275 -0.0614 0.1885 -0.0431 -0.015 0.2417 0.0599 0.2632 -45.684 -1.146 62.926 12 4.8744 0.4689 -1.6989 1.4484 -0.2295 0.6536 -0.0324 -0.1205 -0.4308 0.0304 -0.0869 0.0261 -0.0644 0.0846 0.1194 0.2057 -0.0258 -0.0077 0.1087 0.0237 0.1039 -29.951 -13.017 54.797 13 3.8689 -0.07 -0.3379 3.7757 -0.4322 1.0791 -0.0216 0.2651 -0.3302 -0.1977 -0.0366 0.2845 0.1397 -0.0784 0.0582 0.1857 -0.0651 0.0207 0.0574 -0.0674 0.1735 -38.789 -19.33 49.524 14 2.2086 0.8707 -1.0598 1.3041 -1.0811 1.1064 0.0005 0.0801 0.1348 -0.0268 0.0215 0.0738 -0.0456 -0.1968 -0.022 0.2029 0.064 -0.0157 0.2126 -0.0298 0.116 -33.95 5.159 40.916 15 1.8521 0.2044 -0.1983 0.672 0.0602 0.7065 0.0228 0.2273 0.0145 -0.0036 -0.0182 0.059 0.0644 -0.0757 -0.0047 0.2117 0.0178 -0.0075 0.1732 0.0065 0.0404 -24.942 0.289 30.518 16 0.9248 -0.3155 0.014 0.7826 -0.6626 1.6431 0.0133 0.0554 -0.0683 -0.0737 0.0191 -0.0098 0.0948 -0.0834 -0.0325 0.1884 -0.0088 -0.0155 0.1228 -0.0111 0.087 -16.41 -4.062 36.646 17 2.5371 -0.4446 -0.9029 0.9695 0.6939 3.2322 -0.0313 0.4831 -0.1774 -0.0126 -0.1487 0.2529 -0.0857 -0.3458 0.1799 0.1121 0.1105 -0.0565 0.3172 -0.1042 0.0953 -18.743 -23.767 -3.419 18 2.162 -0.2213 -0.702 0.6984 -0.0716 1.0708 0.135 0.0527 -0.1472 0.0925 -0.2607 0.042 -0.1734 -0.0188 0.1257 0.25 0.0179 -0.0223 0.182 -0.0259 0.0202 -12.635 -20.877 13.465 19 1.3188 -5.0712 -0.4056 24.6023 -8.2054 20.0044 -0.2156 -0.2269 0.0785 1.049 0.0653 -0.4271 -0.0604 1.4796 0.1503 0.1258 -0.0939 -0.0242 0.4323 -0.1004 0.1973 -26.409 -22.796 29.62 20 3.1962 -2.0963 1.3736 4.5784 -0.5951 1.1979 -0.2005 -0.2273 -0.6308 0.1209 0.2232 0.7222 0.0352 -0.0173 -0.0227 0.1473 0.007 0.047 0.1116 0.0535 0.2649 -13.78 -38.047 20.912 21 6.7116 -5.2493 -0.3701 4.9852 0.8184 0.3807 0.2745 0.1249 -1.6943 0.074 -0.3185 1.1754 0.2419 -0.2187 0.044 0.2811 -0.2262 -0.0702 0.2062 -0.0633 0.6484 -22.375 -44.803 15.757 22 3.4857 -0.0998 -0.9593 0.4994 -0.7941 1.746 0.1819 0.5029 -0.2034 0.0504 -0.1538 0.0595 -0.2107 -0.0813 -0.0281 0.2249 0.1143 -0.0244 0.3672 -0.0672 0.0259 -18.382 -20.56 6.062 23 10.4582 -1.2097 -3.6749 0.6026 1.3497 3.2122 -0.0062 1.1511 -0.698 -0.0319 -0.2998 0.1322 -0.016 -0.6099 0.306 0.1519 0.1431 -0.0763 0.4461 -0.1785 0.0952 -19.983 -25.08 -3.139 24 1.7309 -0.5329 0.3704 0.3155 0.258 1.1063 0.0919 0.4854 -0.1903 -0.0638 -0.1894 0.078 -0.1124 -0.0174 0.0975 0.1981 0.0812 -0.0174 0.3274 -0.0489 0.1046 -1.607 -27.142 -2.055 25 1.4685 0.1375 -0.0534 1.7092 -0.5676 1.0503 0.0791 -0.0438 -0.1091 0.0796 -0.1732 -0.3734 -0.0366 0.1865 0.0941 0.0512 0.0154 0.0276 0.1246 0.0185 0.1702 37.171 -29.127 11.433 26 1.602 0.9984 -0.8412 1.0204 -0.7236 1.0226 0.0704 -0.0532 0.1334 0.0117 0.0333 0.0501 -0.1146 0.0043 -0.1038 0.2041 0.027 0.0208 0.1464 -0.0124 0.1223 29.591 -18.979 8.848 27 6.4309 -0.3686 1.8454 2.5365 -1.0095 4.1696 0.0036 -0.4736 0.462 0.2343 -0.1186 -0.0067 -0.4908 -0.004 0.1151 0.2679 -0.0804 -0.0003 0.1052 0.0119 0.1172 44.384 -3.398 0.169 28 4.4779 0.0885 -0.5726 0.0196 -0.1503 1.3215 -0.0444 0.4061 -0.099 0.0082 0.0389 -0.003 -0.013 -0.1828 0.0056 0.201 0.022 0.0455 0.1902 0.0243 0.1237 32.189 -16.497 -9.456 29 4.1617 -0.3998 -1.1128 4.051 0.9983 3.9076 -0.2417 0.4921 -0.7903 -0.1666 0.0776 -0.0884 0.2655 0.125 0.1641 0.1073 0.0113 0.0797 0.167 -0.0608 0.1769 40.381 -22.044 -14.194 30 1.8509 0.7639 -0.723 1.4539 -1.2985 1.1849 -0.0069 -0.0428 0.0145 0.0515 -0.1045 -0.1816 -0.012 0.0894 0.1115 0.1456 0.016 -0.0297 0.1509 -0.0084 0.1574 36.062 -26.795 12.576 31 1.4361 -0.5949 0.0372 1.5861 -0.1496 0.4284 0.0407 0.2242 -0.0918 -0.1285 -0.0491 -0.1281 0.0387 -0.0802 0.0084 0.199 0.0148 0.0181 0.1747 -0.014 0.085 24.285 -35.51 8.318 32 1.3962 -0.2259 0.1998 0.9874 -0.2615 0.9355 0.0234 0.2244 -0.1466 -0.0355 -0.0279 -0.0566 0.0285 -0.0185 0.0045 0.1709 0.0218 0.0197 0.2337 -0.0206 0.0501 19.158 -32.11 5.504
精密化 TLSグループ 大きな表を表示 (5 x 32) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A1 - 41 2 X-RAY DIFFRACTION 2 A42 - 88 3 X-RAY DIFFRACTION 3 A89 - 131 4 X-RAY DIFFRACTION 4 A132 - 155 5 X-RAY DIFFRACTION 5 A156 - 194 6 X-RAY DIFFRACTION 6 A195 - 261 7 X-RAY DIFFRACTION 7 A262 - 363 8 X-RAY DIFFRACTION 8 A364 - 398 9 X-RAY DIFFRACTION 9 B1 - 37 10 X-RAY DIFFRACTION 10 B38 - 91 11 X-RAY DIFFRACTION 11 B92 - 113 12 X-RAY DIFFRACTION 12 B114 - 157 13 X-RAY DIFFRACTION 13 B158 - 195 14 X-RAY DIFFRACTION 14 B196 - 243 15 X-RAY DIFFRACTION 15 B244 - 362 16 X-RAY DIFFRACTION 16 B363 - 398 17 X-RAY DIFFRACTION 17 C2 - 32 18 X-RAY DIFFRACTION 18 C33 - 95 19 X-RAY DIFFRACTION 19 C96 - 110 20 X-RAY DIFFRACTION 20 C112 - 158 21 X-RAY DIFFRACTION 21 C159 - 194 22 X-RAY DIFFRACTION 22 C195 - 246 23 X-RAY DIFFRACTION 23 C247 - 303 24 X-RAY DIFFRACTION 24 C304 - 397 25 X-RAY DIFFRACTION 25 D2 - 39 26 X-RAY DIFFRACTION 26 D40 - 94 27 X-RAY DIFFRACTION 27 D95 - 114 28 X-RAY DIFFRACTION 28 D115 - 155 29 X-RAY DIFFRACTION 29 D156 - 194 30 X-RAY DIFFRACTION 30 D195 - 261 31 X-RAY DIFFRACTION 31 D292 - 359 32 X-RAY DIFFRACTION 32 D360 - 398