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 SHARP位相決定 Show 直接法5 位相決定 Show REFMAC5.2.0019精密化 Show PDB_EXTRACT3 データ抽出 Show MAR345CCDデータ収集 HKL-2000データ削減
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 2.79→46.554 Å / Cor.coef. Fo :Fc : 0.936 / Cor.coef. Fo :Fc free : 0.903 / WRfactor Rfree : 0.275 / WRfactor Rwork : 0.217 / SU B : 29.187 / SU ML : 0.259 / TLS residual ADP flag : LIKELY RESIDUAL / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.546 / ESU R Free : 0.326 / 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 0.261 842 5.083 % RANDOM Rwork 0.209 - - - obs 0.212 16565 98.901 % -
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 : 35.398 Å2 Baniso -1 Baniso -2 Baniso -3 1- 2.783 Å2 1.391 Å2 0 Å2 2- - 2.783 Å2 0 Å2 3- - - -4.174 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.79→46.554 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3014 0 0 13 3027
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_d0.009 0.022 3079 X-RAY DIFFRACTION r_angle_refined_deg1.191 1.955 4196 X-RAY DIFFRACTION r_dihedral_angle_1_deg6.166 5 379 X-RAY DIFFRACTION r_dihedral_angle_2_deg36.716 22.794 136 X-RAY DIFFRACTION r_dihedral_angle_3_deg18.668 15 477 X-RAY DIFFRACTION r_dihedral_angle_4_deg13.779 15 29 X-RAY DIFFRACTION r_chiral_restr0.081 0.2 486 X-RAY DIFFRACTION r_gen_planes_refined0.003 0.02 2333 X-RAY DIFFRACTION r_nbd_refined0.215 0.2 1337 X-RAY DIFFRACTION r_nbtor_refined0.308 0.2 2027 X-RAY DIFFRACTION r_xyhbond_nbd_refined0.128 0.2 99 X-RAY DIFFRACTION r_symmetry_vdw_refined0.153 0.2 30 X-RAY DIFFRACTION r_symmetry_hbond_refined0.07 0.2 3 X-RAY DIFFRACTION r_mcbond_it0.381 1.5 1972 X-RAY DIFFRACTION r_mcangle_it0.715 2 3110 X-RAY DIFFRACTION r_scbond_it1.013 3 1240 X-RAY DIFFRACTION r_scangle_it1.751 4.5 1086
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 (%)2.79-2.863 0.317 55 0.357 1032 1222 88.953 2.863-2.941 0.418 69 0.333 1092 1189 97.645 2.941-3.026 0.355 76 0.28 1069 1150 99.565 3.026-3.119 0.218 49 0.247 1060 1114 99.551 3.119-3.221 0.253 57 0.238 1049 1109 99.729 3.221-3.334 0.308 58 0.218 984 1043 99.904 3.334-3.46 0.235 50 0.207 978 1030 99.806 3.46-3.601 0.21 49 0.194 939 988 100 3.601-3.761 0.225 55 0.192 878 933 100 3.761-3.944 0.231 46 0.186 850 896 100 3.944-4.157 0.176 43 0.192 837 881 99.886 4.157-4.409 0.221 40 0.18 760 800 100 4.409-4.712 0.222 46 0.143 735 781 100 4.712-5.089 0.216 24 0.16 696 720 100 5.089-5.573 0.249 27 0.207 641 668 100 5.573-6.227 0.386 26 0.229 583 609 100 6.227-7.185 0.366 34 0.238 516 550 100 7.185-8.786 0.266 16 0.194 449 465 100 8.786-12.366 0.215 11 0.177 361 372 100 12.366-46.554 0.355 11 0.337 214 229 98.253
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 15.466 4.0077 -4.033 6.309 6.9846 13.2849 -0.1896 -0.768 1.8711 1.5818 -0.0472 -0.0042 -1.3613 1.0468 0.2369 0.0772 -0.138 -0.1008 -0.0791 -0.0557 0.7785 34.1957 67.8513 -13.0905 2 15.5443 -3.4775 -4.2514 14.9473 -2.012 1.7824 0.3588 1.7308 2.1275 0.3532 -0.2008 -1.267 -2.3105 0.9028 -0.158 0.1996 -0.1166 0.1178 0.2629 0.4051 0.6164 31.8873 66.1336 -25.8257 3 4.1669 -3.1284 -1.0393 3.6508 1.8211 6.3801 0.2903 0.4584 1.195 -0.1862 -0.436 -0.2977 -0.6455 -0.2605 0.1456 0.0705 0.0552 0.0593 0.2493 0.2015 0.4687 23.3728 60.6505 -20.7744 4 7.9702 3.993 -3.867 29.474 2.912 6.6775 -0.3585 -0.8317 1.0935 1.0025 0.6148 -0.7765 -0.5334 0.5337 -0.2563 0.1604 0.108 -0.0281 0.3397 -0.0451 0.2087 23.587 56.4163 -9.183 5 5.8016 3.6747 -0.2104 6.1397 -5.2115 6.7723 -0.0588 0.2468 0.0459 0.083 -0.0811 0.757 -0.1587 0.091 0.1399 0.0968 0.1631 0.037 0.3799 0.0812 0.1931 20.5154 51.4492 -18.0095 6 17.5556 -3.995 -2.4232 7.4315 -3.3715 2.922 0.2776 0.7895 0.1199 -0.08 -0.121 0.4706 0.0697 -0.3656 -0.1566 0.1319 0.1511 0.0276 0.3823 -0.009 0.1145 20.5618 51.1431 -24.4947 7 6.4595 0.417 -4.1644 6.3867 -4.0218 4.8994 0.3943 0.8761 -0.8823 -0.3739 -0.2569 0.3464 0.5038 0.2677 -0.1374 0.0858 0.1767 0.0035 0.5864 -0.151 0.1693 28.0752 44.8384 -28.0302 8 12.8722 4.3251 4.6274 7.9735 2.7246 11.7254 0.9751 1.9596 1.0144 -0.7104 -0.7152 0.0162 -0.4392 0.0205 -0.2599 0.0619 0.1009 0.2361 0.624 0.3682 0.2255 28.666 55.968 -32.7346 9 7.6411 -10.028 -5.683 18.6201 0.931 12.0303 0.5994 2.1244 0.8835 -0.0765 -0.7285 -0.4482 1.8131 0.5711 0.1291 0.0396 0.1345 0.0399 0.9137 0.0143 0.2364 35.9812 45.2429 -34.3026 10 15.8 5.775 -0.9371 10.6371 5.8318 5.5781 0.1372 1.7064 1.4656 -1.6215 -0.2707 -0.3528 -1.2168 0.2009 0.1334 0.1491 0.1127 0.1547 0.8151 0.4508 0.3325 34.1911 56.0681 -35.0637 11 8.4824 -2.3103 1.1791 1.5224 -3.108 8.8594 -0.0505 -0.2661 -0.619 0.197 -0.1914 -0.3442 0.0117 0.7541 0.2419 0.1822 -0.0674 0.0209 0.3907 0.0043 0.2563 2.2566 61.5194 -25.4882 12 1.6272 0.7744 -0.6172 1.2001 1.5534 4.3367 0.1101 -0.2292 0.3556 -0.1014 -0.0546 0.2077 -0.6949 -0.1481 -0.0555 0.3281 -0.0172 0.0189 0.2456 -0.0219 0.2453 -7.1093 67.9815 -23.7235 13 4.3356 2.2005 -1.0698 4.4232 -5.2603 13.4962 -0.0446 -0.3357 0.0748 0.2177 0.2639 -0.2866 -0.3971 0.0805 -0.2193 0.0919 -0.0206 -0.0332 0.4369 -0.1512 0.1369 -5.9924 62.3916 -12.0822 14 15.4919 6.3127 -2.0839 8.2517 -0.6973 9.3881 0.3601 -1.1039 0.5322 0.4912 -0.1203 -0.2043 -0.6275 0.6753 -0.2397 0.1879 0.0761 -0.0331 0.403 0.0565 0.0421 -5.065 63.6412 -10.7746 15 6.1202 6.312 8.179 46.7336 -2.0882 13.6834 -0.6249 -0.9629 0.2893 1.3927 1.1132 0.5674 -1.6087 -0.363 -0.4884 0.3434 0.1449 0.2266 1.0723 -0.2367 0.3365 -17.8063 67.4473 -6.2906 16 1.7355 2.4092 0.0133 6.1749 -3.9646 6.8257 -0.1175 -0.3088 -0.0983 -0.0355 0.2551 0.543 0.1744 -0.6286 -0.1375 0.0589 -0.0066 -0.0087 0.4846 -0.005 0.2125 -18.7591 58.1437 -19.2841 17 11.6385 3.7423 1.4269 2.7067 2.4065 20.1711 -0.184 -0.297 1.6874 0.5866 0.0917 0.7772 -1.8627 -1.1637 0.0923 0.0772 0.2468 0.0931 0.4155 -0.0506 0.4377 -23.8279 70.6761 -17.6451 18 4.1972 -2.9938 -4.2272 4.5002 6.6398 11.3613 -0.4577 -0.0681 -0.4512 -0.2804 0.3719 0.345 0.5318 -0.3797 0.0859 0.2137 -0.0742 -0.0504 0.3568 0.1034 0.2668 -18.3916 54.9664 -30.7685 19 16.4671 4.0527 -10.9352 4.5198 0.3268 12.9043 -0.0923 0.5355 0.1211 -0.2659 0.3029 0.4317 -0.4856 -0.7223 -0.2106 0.1788 0.0416 -0.0882 0.3833 0.1296 0.1364 -20.2406 61.0285 -30.7806 20 25.8048 -5.6184 -10.0059 3.1361 2.0642 4.2713 0.0704 0.1509 0.8932 -0.5643 0.154 0.4519 -0.5828 -0.5381 -0.2244 0.21 0.0361 -0.0828 0.371 0.1248 0.2354 -19.5586 63.1468 -29.7774
精密化 TLSグループ 大きな表を表示 (7 x 20) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA29 - 50 29 - 50 2 X-RAY DIFFRACTION 2 AA62 - 80 62 - 80 3 X-RAY DIFFRACTION 3 AA81 - 109 81 - 109 4 X-RAY DIFFRACTION 4 AA110 - 128 110 - 128 5 X-RAY DIFFRACTION 5 AA139 - 149 139 - 149 6 X-RAY DIFFRACTION 6 AA150 - 174 150 - 174 7 X-RAY DIFFRACTION 7 AA175 - 192 175 - 192 8 X-RAY DIFFRACTION 8 AA193 - 207 193 - 207 9 X-RAY DIFFRACTION 9 AA216 - 228 216 - 228 10 X-RAY DIFFRACTION 10 AA229 - 265 229 - 265 11 X-RAY DIFFRACTION 11 BB29 - 67 29 - 67 12 X-RAY DIFFRACTION 12 BB68 - 97 68 - 97 13 X-RAY DIFFRACTION 13 BB98 - 119 98 - 119 14 X-RAY DIFFRACTION 14 BB120 - 148 120 - 148 15 X-RAY DIFFRACTION 15 BB149 - 162 149 - 162 16 X-RAY DIFFRACTION 16 BB163 - 185 163 - 185 17 X-RAY DIFFRACTION 17 BB186 - 196 186 - 196 18 X-RAY DIFFRACTION 18 BB197 - 221 197 - 221 19 X-RAY DIFFRACTION 19 BB222 - 240 222 - 240 20 X-RAY DIFFRACTION 20 BB256 - 265 256 - 265