ソフトウェア 名称 バージョン 分類 REFMAC精密化 Aimless0.5.15データスケーリング PDB_EXTRACT3.22 データ抽出 iMOSFLMデータ削減 PHASER位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 5U5I解像度 : 2.1→61.75 Å / Cor.coef. Fo :Fc : 0.946 / Cor.coef. Fo :Fc free : 0.9 / WRfactor Rfree : 0.2413 / WRfactor Rwork : 0.1941 / FOM work R set : 0.6957 / SU B : 20.101 / SU ML : 0.247 / SU R Cruickshank DPI : 0.282 / SU Rfree : 0.2261 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.282 / ESU R Free : 0.226 / 立体化学のターゲット値 : MAXIMUM LIKELIHOOD詳細 : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDEDRfactor 反射数 %反射 Selection details Rfree 0.2779 1646 5.1 % RANDOM Rwork 0.2246 - - - obs 0.2274 30538 99.94 % -
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 max : 95.59 Å2 / Biso mean : 41.225 Å2 / Biso min : 22.08 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.29 Å2 -0 Å2 -0 Å2 2- - -0.75 Å2 0 Å2 3- - - 1.05 Å2
精密化ステップ サイクル : final / 解像度 : 2.1→61.75 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4181 0 89 144 4414 Biso mean - - 43.59 39.18 - 残基数 - - - - 556
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.013 0.019 4359 X-RAY DIFFRACTION r_bond_other_d0.002 0.02 4088 X-RAY DIFFRACTION r_angle_refined_deg1.683 1.992 5922 X-RAY DIFFRACTION r_angle_other_deg0.983 3 9464 X-RAY DIFFRACTION r_dihedral_angle_1_deg5.869 5 558 X-RAY DIFFRACTION r_dihedral_angle_2_deg39.211 24.483 174 X-RAY DIFFRACTION r_dihedral_angle_3_deg15.048 15 722 X-RAY DIFFRACTION r_dihedral_angle_4_deg9.848 15 24 X-RAY DIFFRACTION r_chiral_restr0.094 0.2 689 X-RAY DIFFRACTION r_gen_planes_refined0.006 0.021 4852 X-RAY DIFFRACTION r_gen_planes_other0.001 0.02 854
Refine LS restraints NCS Ens-ID : 1 / 数 : 16486 / Refine-ID : X-RAY DIFFRACTION / タイプ : interatomic distance / Rms dev position : 0.08 Å / Weight position : 0.05
LS精密化 シェル 解像度 : 2.1→2.155 Å / Rfactor Rfree error : 0 / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.374 107 - Rwork 0.343 2206 - all - 2313 - obs - - 99.61 %
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 16) 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 6.1232 -1.7302 -2.1485 2.8775 1.5224 5.6904 -0.001 -0.0165 -0.2294 0.0549 -0.0612 0.1377 0.1278 -0.0763 0.0622 0.3871 -0.0267 0.0197 0.1482 0.0136 0.0198 -4.0289 -11.0077 25.231 2 10.2383 0.1345 -1.6002 3.0892 1.2504 3.9494 -0.0301 -1.0416 -0.3327 0.4968 0.0228 -0.0045 0.1289 0.3246 0.0073 0.5719 0.0362 0.0022 0.332 0.0593 0.0551 -2.1727 -11.6375 34.977 3 7.0525 -0.3582 -2.545 1.2898 -1.0903 2.1185 -0.0176 -0.4815 0.9177 0.7123 0.086 -0.297 -0.5921 0.1078 -0.0684 0.6344 0.0478 -0.0843 0.2304 -0.1015 0.1876 2.1082 0.2902 28.5187 4 2.9543 -2.5737 -1.9093 8.1115 0.5946 4.3058 0.2857 0.1269 1.4252 0.4699 -0.1259 -0.7722 -0.7063 -0.0802 -0.1597 0.5865 0.0154 0.0682 0.1204 0.0456 0.9754 4.4836 5.9573 22.0288 5 2.8951 2.8135 -2.266 12.1261 -9.1877 9.0245 -0.1833 -0.4011 0.1476 0.0529 0.0486 -0.1241 -0.7511 0.0875 0.1347 0.4292 0.0219 -0.0248 0.3194 -0.0248 0.057 -2.1356 4.6066 2.3974 6 3.6602 1.0617 -2.1689 3.0644 -1.1552 3.1542 0.0087 -0.5523 -0.0517 0.2527 -0.1929 0.1567 -0.8336 0.0742 0.1842 0.7598 0.0444 -0.0281 0.2501 -0.0431 0.0368 -12.89 11.9785 0.595 7 3.5783 2.9497 -2.9999 8.9106 -5.3892 17.9379 -0.0454 -0.1752 -0.0039 -0.0373 0.0695 -0.1383 -0.2433 0.4305 -0.0241 0.36 -0.0125 -0.0045 0.2292 -0.0796 0.2674 -7.197 14.1981 0.9675 8 1.4186 -0.5606 2.3777 1.9106 -0.7857 4.0052 -0.1183 -0.2357 0.0132 -0.0776 0.0887 0.1052 -0.2631 -0.3803 0.0296 0.5448 0.0265 0.0369 0.2414 -0.0043 0.0114 -8.9476 1.5032 6.7686 9 6.7774 0.6215 -1.3617 8.3459 -0.6185 4.9479 0.1621 0.2297 0.2929 0.3523 0.0806 0.3245 -0.0961 0.0238 -0.2427 0.4577 0.0574 -0.0172 0.1611 0.007 0.0326 -5.3317 15.0088 -35.1084 10 7.5724 3.5804 3.569 3.436 1.0725 1.9838 -0.0681 0.9776 -0.0031 -0.5404 0.1624 0.0693 0.1143 0.4181 -0.0943 0.597 0.1098 -0.0102 0.4785 0.0558 0.0983 -2.6596 14.915 -44.8302 11 5.038 1.295 2.5344 7.3794 0.3372 3.1509 0.2733 0.1402 -0.7615 -0.1611 -0.2055 -0.7754 0.2235 0.3755 -0.0677 0.4487 0.0034 -0.0509 0.2123 0.0124 0.2193 6.3362 4.9646 -32.5185 12 6.1988 -4.7387 6.4627 8.6581 -9.6946 12.8367 -0.316 -0.0055 0.122 0.7408 -0.0524 -0.1756 -0.583 0.3691 0.3683 0.5645 -0.1027 -0.0741 0.1864 -0.0032 0.1113 -2.1992 4.3439 -12.1894 13 6.9513 -0.4475 3.5188 2.4944 -0.384 4.0154 -0.1138 0.6869 -0.2036 -0.5382 0.0307 0.3582 -0.0209 0.7629 0.0831 0.5129 -0.0468 -0.0152 0.1908 -0.0089 0.1141 -7.6652 -6.7253 -10.2471 14 5.944 -2.4867 4.0773 3.9184 -1.593 5.1564 0.0757 0.3383 -0.6329 -0.3448 0.0869 0.5371 -0.0976 0.1299 -0.1626 0.4549 -0.0437 -0.0001 0.1317 -0.0362 0.1292 -13.4878 -5.8838 -15.1815 15 1.7002 0.6482 -2.1435 1.9978 -2.3337 4.3542 0.1019 -0.2343 -0.0626 0.1663 -0.2044 -0.0369 -0.5849 0.374 0.1026 0.7337 -0.0677 -0.07 0.1682 -0.0112 0.0174 -1.3823 8.1425 -16.3756 16 6.4657 10.4844 4.0627 17.0108 6.6002 2.5687 -0.5549 -0.145 1.1014 -0.9683 -0.1808 1.8172 -0.4334 -0.0316 0.7358 1.1531 -0.1411 -0.2547 0.6335 0.0576 0.3508 1.119 18.6549 -16.3382
精密化 TLSグループ 大きな表を表示 (5 x 16) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A10 - 49 2 X-RAY DIFFRACTION 2 A50 - 83 3 X-RAY DIFFRACTION 3 A84 - 110 4 X-RAY DIFFRACTION 4 A111 - 137 5 X-RAY DIFFRACTION 5 A138 - 154 6 X-RAY DIFFRACTION 6 A155 - 178 7 X-RAY DIFFRACTION 7 A179 - 194 8 X-RAY DIFFRACTION 8 A195 - 288 9 X-RAY DIFFRACTION 9 B11 - 49 10 X-RAY DIFFRACTION 10 B50 - 82 11 X-RAY DIFFRACTION 11 B83 - 136 12 X-RAY DIFFRACTION 12 B137 - 152 13 X-RAY DIFFRACTION 13 B153 - 178 14 X-RAY DIFFRACTION 14 B179 - 230 15 X-RAY DIFFRACTION 15 B231 - 282 16 X-RAY DIFFRACTION 16 B283 - 287