ソフトウェア 名称 バージョン 分類 NB DENZOデータ削減 Show SCALEPACKデータスケーリング Show 直接法5 位相決定 Show MOLREP位相決定 Show REFMAC5.2.0005精密化 Show PDB_EXTRACT2 データ抽出 Show HKL-2000データ削減
精密化 構造決定の手法 : 分子置換開始モデル : 2AQJ monomer with no ligands解像度 : 2.494→29.129 Å / Cor.coef. Fo :Fc : 0.958 / Cor.coef. Fo :Fc free : 0.932 / WRfactor Rfree : 0.204 / WRfactor Rwork : 0.159 / SU B : 12.078 / SU ML : 0.142 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.267 / ESU R Free : 0.209 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD / 詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor 反射数 %反射 Selection details Rfree 0.208 3008 5.045 % RANDOM Rwork 0.161 - - - obs 0.164 59619 99.921 % -
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 BULK SOLVENT原子変位パラメータ Biso mean : 2.559 Å2 Baniso -1 Baniso -2 Baniso -3 1- 0.995 Å2 0.498 Å2 0 Å2 2- - 0.995 Å2 0 Å2 3- - - -1.493 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.494→29.129 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 8437 0 10 455 8902
拘束条件 大きな表を表示 (5 x 17) 大きな表を隠す Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.014 0.022 8678 X-RAY DIFFRACTION r_angle_refined_deg1.407 1.936 11779 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.012 5 1048 X-RAY DIFFRACTION r_dihedral_angle_2_deg34.102 23.224 456 X-RAY DIFFRACTION r_dihedral_angle_3_deg14.825 15 1365 X-RAY DIFFRACTION r_dihedral_angle_4_deg18.633 15 74 X-RAY DIFFRACTION r_chiral_restr0.1 0.2 1224 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.02 6856 X-RAY DIFFRACTION r_nbd_refined0.203 0.2 3879 X-RAY DIFFRACTION r_nbtor_refined0.312 0.2 6015 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.141 0.2 577 X-RAY DIFFRACTION r_symmetry_vdw_refined0.153 0.2 32 X-RAY DIFFRACTION r_symmetry_hbond_refined0.246 0.2 2 X-RAY DIFFRACTION r_mcbond_it0.195 1.5 5325 X-RAY DIFFRACTION r_mcangle_it0.251 2 8398 X-RAY DIFFRACTION r_scbond_it1.1 3 3802 X-RAY DIFFRACTION r_scangle_it1.853 4.5 3381
Refine LS restraints NCS Dom-ID : 1 / Auth asym-ID : A / Ens-ID : 1 / 数 : 4209 / Refine-ID : X-RAY DIFFRACTION
タイプ Rms dev position (Å)Weight position MEDIUM POSITIONAL0.25 0.5 MEDIUM THERMAL0.3 2
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 20
大きな表を表示 (7 x 20) 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 (%)2.494-2.559 0.267 219 0.221 4180 4407 99.818 2.559-2.629 0.235 186 0.199 4072 4258 100 2.629-2.705 0.278 231 0.206 3953 4184 100 2.705-2.788 0.261 229 0.195 3831 4060 100 2.788-2.88 0.253 188 0.193 3736 3924 100 2.88-2.981 0.234 206 0.176 3589 3795 100 2.981-3.093 0.239 170 0.176 3523 3693 100 3.093-3.219 0.239 187 0.17 3327 3514 100 3.219-3.362 0.208 155 0.162 3235 3390 100 3.362-3.526 0.198 152 0.151 3071 3223 100 3.526-3.717 0.203 170 0.156 2932 3102 100 3.717-3.942 0.198 144 0.146 2773 2917 100 3.942-4.214 0.157 136 0.128 2600 2736 100 4.214-4.55 0.16 111 0.128 2453 2564 100 4.55-4.984 0.187 129 0.132 2234 2363 100 4.984-5.57 0.193 132 0.15 1984 2116 100 5.57-6.429 0.24 75 0.182 1816 1891 100 6.429-7.865 0.193 92 0.169 1492 1584 100 7.865-11.089 0.139 65 0.126 1178 1243 100 11.089-29.129 0.141 31 0.172 632 702 94.444
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 20) 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 3.0648 1.1436 1.6653 1.351 0.603 2.7388 0.146 -0.1192 -0.3145 0.2335 -0.1518 -0.0973 0.6014 0.0083 0.0058 0.0541 -0.0516 0.074 -0.0767 0.0287 -0.0175 -21.7857 24.1705 5.9291 2 16.7579 -5.0082 -3.2383 8.7561 0.3454 10.8738 -0.3207 -0.0453 -0.553 0.2339 0.3569 -0.5481 1.4214 1.4387 -0.0362 0.2547 0.0515 0.0529 0.213 -0.1349 -0.0659 -23.4713 18.595 -24.3333 3 2.2285 0.5965 1.1313 1.1223 0.3549 1.6021 0.0407 0.1805 -0.3177 0.0745 -0.1061 -0.0514 0.8968 0.1874 0.0653 0.2134 -0.0312 0.1086 -0.0469 -0.0145 0.0717 -23.2373 15.1988 -1.5985 4 2.0274 0.128 2.4869 0.9935 -0.1862 7.216 0.0468 -0.3328 0.1555 0.396 -0.1628 0.021 -0.2559 0.0633 0.116 -0.0464 -0.1086 0.0313 -0.0066 0.0083 -0.0286 -15.5382 45.6112 18.0693 5 1.1592 -0.4199 0.1236 3.3053 -0.4019 3.2503 -0.0558 -0.0969 -0.1337 0.4349 0.0247 0.4125 0.3952 -0.4571 0.031 -0.0248 -0.1773 0.1008 0.0278 -0.0165 -0.0209 -39.5678 25.0127 6.9906 6 1.5392 0.9713 0.3757 1.974 -0.0825 2.422 -0.0506 0.0259 0.0457 0.0979 -0.0839 0.0078 0.2012 0.1819 0.1345 -0.1471 -0.0285 0.0085 -0.0352 0.0326 -0.0969 -15.8364 39.1049 3.5485 7 2.1044 0.5175 0.1835 0.5 0.4647 4.2916 -0.0949 0.4901 0.3976 -0.1235 0.065 0.0993 -0.1185 -0.0713 0.0299 -0.1013 -0.0784 0.0166 -0.0004 0.0018 -0.0197 -32.449 36.5597 -10.3402 8 8.5541 0.3908 11.4827 0.3842 -0.7337 19.7365 0.5056 0.1024 -0.9749 -0.3721 -0.0445 -0.4796 1.6971 1.028 -0.4611 0.3159 0.011 0.0586 0.4235 -0.0574 0.3143 -15.2985 25.8406 -13.1942 9 1.6833 0.8132 -0.3199 0.3939 -0.2497 8.3996 -0.2793 0.3592 -0.3 -0.0888 0.1784 -0.1154 1.1016 0.6044 0.1009 0.1524 -0.0443 0.0931 0.1417 -0.09 0.0167 -26.2058 20.4125 -23.5666 10 3.5974 0.1427 0.3367 10.8568 -4.5337 28.1928 -0.0914 0.1677 -1.2502 -0.0764 -0.3638 0.0501 2.6029 0.8116 0.4552 0.1932 0.0992 0.1405 0.1614 -0.0718 0.2663 -26.2915 2.1567 -3.1619 11 6.2864 -0.1756 1.409 1.1595 0.1794 1.8472 0.0206 0.5403 -0.1809 -0.1275 0.017 0.0232 0.2663 -0.1165 -0.0376 -0.1044 -0.0169 0.022 0.0818 -0.1001 -0.0265 -6.7274 30.0661 -42.1759 12 4.9754 3.2335 2.2191 6.4237 2.8291 4.4729 0.1946 0.0375 -0.4206 0.42 0.006 -0.1148 0.5017 0.3088 -0.2006 -0.2616 0.0964 0.0263 0.0205 0.038 -0.0738 15.8438 36.4153 -26.9981 13 11.7559 6.893 0.8727 17.0031 0.8458 7.0707 0.1115 -0.3488 -0.622 -0.03 -0.2022 -0.1398 1.0652 0.0052 0.0907 0.0458 0.0048 0.0446 0.1628 0.1009 -0.1121 8.747 33.3114 -3.8491 14 2.5665 -0.2985 0.8993 0.5384 0.0329 1.7775 0.0624 0.3274 -0.1049 -0.0311 -0.0699 0.0296 0.2334 -0.0174 0.0074 -0.1448 -0.0426 0.0623 0.0468 0.0126 -0.0176 -1.9736 35.0334 -38.077 15 2.5431 -0.282 -0.3161 2.3497 0.1696 3.1153 0.0492 0.399 0.1414 -0.163 -0.072 -0.0356 -0.0419 0.2533 0.0227 -0.2533 -0.0172 -0.0028 0.1162 0.0167 -0.1034 15.7176 45.9428 -37.2621 16 4.9748 0.2771 0.5998 1.1733 -0.1154 1.1917 0.0148 0.029 0.0864 0.0659 -0.0369 0.1164 0.1229 -0.2019 0.0221 -0.1814 -0.0352 0.0334 0.0706 -0.0279 -0.074 -11.5397 39.6865 -33.2361 17 2.9808 1.0545 0.1109 0.3735 0.0006 3.1829 0.0973 -0.3203 0.5336 0.1479 -0.0555 0.398 -0.1169 -0.2471 -0.0418 -0.1819 0.0317 0.0357 0.0466 -0.0043 0.0139 3.2697 50.741 -20.0174 18 8.1116 5.5771 9.934 4.4776 8.9431 19.1087 0.178 -0.1686 -0.9891 0.4503 0.2738 -0.0546 1.5712 -0.137 -0.4517 0.2668 -0.1259 0.0605 0.3327 0.0943 0.3084 -2.5975 30.7055 -16.3655 19 2.0116 -0.2269 -1.0223 1.0402 0.0645 7.113 0.0495 -0.4296 -0.241 0.0681 -0.133 0.0715 0.7794 0.0762 0.0835 -0.0759 -0.0251 0.0332 0.1364 0.0648 0.0051 8.4387 34.91 -6.3259 20 5.7435 0.7503 -3.6117 12.873 4.0402 24.5029 -0.3321 0.1866 -0.5505 -0.042 -0.2254 -0.3429 1.9652 1.0969 0.5575 0.0827 0.2137 0.0912 0.0533 0.0572 0.1666 21.2738 20.4998 -27.0163
精密化 TLSグループ Refine-ID : X-RAY DIFFRACTION / Selection : ALL
大きな表を表示 (6 x 20) 大きな表を隠す ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 1 AA12 - 120 32 - 140 2 2 AA121 - 138 141 - 158 3 3 AA139 - 199 159 - 219 4 4 AA200 - 254 220 - 274 5 5 AA255 - 336 275 - 356 6 6 AA337 - 398 357 - 418 7 7 AA399 - 446 419 - 466 8 8 AA447 - 473 467 - 493 9 9 AA474 - 517 494 - 537 10 10 AA518 - 526 538 - 546 11 11 BB12 - 75 32 - 95 12 12 BB76 - 122 96 - 142 13 13 BB123 - 140 143 - 160 14 14 BB141 - 254 161 - 274 15 15 BB255 - 337 275 - 357 16 16 BB338 - 400 358 - 420 17 17 BB401 - 446 421 - 466 18 18 BB447 - 472 467 - 492 19 19 BB473 - 517 493 - 537 20 20 BB518 - 528 538 - 548