ソフトウェア 名称 バージョン 分類 REFMAC5.8.0189精密化 SCALA3.3.22データスケーリング PHASER位相決定 PDB_EXTRACT3.25 データ抽出 iMOSFLMデータ削減
精密化 構造決定の手法 : 分子置換開始モデル : 5UY1解像度 : 2→122.58 Å / Cor.coef. Fo :Fc : 0.968 / Cor.coef. Fo :Fc free : 0.954 / WRfactor Rfree : 0.2433 / WRfactor Rwork : 0.2005 / FOM work R set : 0.7524 / SU B : 10.639 / SU ML : 0.135 / SU R Cruickshank DPI : 0.1419 / SU Rfree : 0.1381 / 交差検証法 : THROUGHOUT / σ(F) : 0 / ESU R : 0.142 / ESU R Free : 0.138 / 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 0.2255 4438 4.9 % RANDOM Rwork 0.1857 - - - obs 0.1877 86312 98.25 % -
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 : 165.37 Å2 / Biso mean : 52.533 Å2 / Biso min : 28.94 Å2 Baniso -1 Baniso -2 Baniso -3 1- -1.16 Å2 0 Å2 0.09 Å2 2- - -0.75 Å2 0 Å2 3- - - 1.9 Å2
精密化ステップ サイクル : final / 解像度 : 2→122.58 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 7420 0 110 203 7733 Biso mean - - 84.58 47.8 - 残基数 - - - - 928
拘束条件 Refine-ID タイプ Dev ideal Dev ideal target 数 X-RAY DIFFRACTION r_bond_refined_d0.026 0.019 7724 X-RAY DIFFRACTION r_bond_other_d0.002 0.02 7086 X-RAY DIFFRACTION r_angle_refined_deg2.44 1.956 10492 X-RAY DIFFRACTION r_angle_other_deg1.285 2.983 16456 X-RAY DIFFRACTION r_dihedral_angle_1_deg7.406 5 924 X-RAY DIFFRACTION r_dihedral_angle_2_deg33.783 24.136 382 X-RAY DIFFRACTION r_dihedral_angle_3_deg16.937 15 1268 X-RAY DIFFRACTION r_dihedral_angle_4_deg21.358 15 54 X-RAY DIFFRACTION r_chiral_restr0.163 0.2 1108 X-RAY DIFFRACTION r_gen_planes_refined0.014 0.021 8568 X-RAY DIFFRACTION r_gen_planes_other0.002 0.02 1582
LS精密化 シェル 解像度 : 2→2.052 Å / Rfactor Rfree error : 0 / Total num. of bins used : 20 Rfactor 反射数 %反射 Rfree 0.362 323 - Rwork 0.362 6270 - all - 6593 - obs - - 96.91 %
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 3.059 1.996 -2.0886 2.1199 -2.072 2.0479 0.0166 0.0491 -0.1307 -0.0714 -0.0356 0.0289 0.0485 0.0386 0.019 0.1483 -0.0197 0.0145 0.0477 -0.0179 0.1964 11.079 38.154 75.996 2 1.5921 -3.7662 2.3335 15.1139 7.2582 29.7974 -0.1884 -0.0829 -0.0712 0.7658 -0.0454 0.3268 0.4566 -0.681 0.2338 0.1277 -0.0802 0.0324 0.1812 -0.0709 0.04 14.5466 31.2902 60.7087 3 0.6256 -0.3899 -0.6199 0.92 -0.045 0.8898 0.0778 -0.3586 0.2045 0.1119 0.2441 0.053 -0.1804 0.3401 -0.3219 0.0794 -0.0382 0.0146 0.208 -0.1168 0.2147 16.025 24.7376 45.0532 4 2.2762 0.9382 -0.761 2.4985 1.0911 1.8114 -0.4554 -0.577 -0.3126 0.1745 0.2263 0.2043 0.3982 0.5174 0.2291 0.2027 0.1836 0.045 0.2521 0.1668 0.2158 10.2776 4.5467 50.3778 5 3.7212 4.2196 2.5054 5.694 4.8665 6.5898 -0.2058 -0.1232 -0.3212 0.1566 0.0188 -0.2538 0.6398 0.2021 0.1871 0.2007 0.0869 0.0155 0.0549 0.043 0.2502 17.6347 -3.0227 41.1947 6 1.1972 -0.0306 -0.759 0.5396 -0.0716 0.9352 -0.0554 -0.1031 -0.0953 -0.0845 0.0738 -0.0296 0.068 0.0867 -0.0184 0.0962 0.0107 -0.0332 0.0242 -0.0171 0.2196 13.5045 11.3174 33.7627 7 1.2299 1.1828 3.4568 1.1493 3.3153 9.7994 0.2497 0.1742 -0.0869 0.2582 0.1132 -0.0562 0.8129 0.5238 -0.363 0.2085 0.1002 -0.0359 0.2449 -0.0524 0.2043 13.9949 21.3339 65.9808 8 1.8315 0.8363 -0.2146 1.0288 -0.3619 0.1433 0.2609 -0.1805 0.0384 -0.0098 -0.1861 0.0956 0.0059 0.0793 -0.0748 0.1124 -0.0328 0.0141 0.0587 -0.0697 0.2042 7.2102 30.7691 86.2387 9 1.8527 0.8616 2.7303 1.7402 -0.0243 5.3473 0.0997 0.0339 -0.0514 0.1235 0.1314 0.0368 0.148 -0.0867 -0.2312 0.1473 0.0063 -0.0561 0.0388 -0.0032 0.2035 2.5987 42.2963 73.7193 10 2.7092 -0.2941 0.133 0.7762 -0.4767 1.1315 -0.0927 0.2878 0.2805 0.1172 -0.1162 -0.0418 -0.2183 0.1819 0.209 0.1564 -0.0427 -0.0546 0.0562 0.0534 0.1642 12.8191 49.9831 73.806 11 2.144 2.0869 0.9548 2.2756 1.2734 0.9251 -0.0361 0.041 0.0816 -0.0371 -0.0368 0.0604 -0.001 -0.083 0.0729 0.1286 0.0383 -0.0132 0.0453 0.0412 0.2663 30.8961 26.4791 136.7338 12 0.0537 -0.386 -0.7754 2.845 5.7437 11.6139 -0.0463 0.0424 -0.0151 0.2451 -0.2652 0.1464 0.4541 -0.5557 0.3115 0.2027 -0.0205 0.0271 0.312 0.0561 0.102 28.8231 33.6916 121.9078 13 0.3616 -0.4114 0.5048 1.0725 -0.5603 0.8622 0.0878 -0.2948 -0.117 0.0922 0.2212 -0.0136 0.119 -0.3627 -0.309 0.0941 -0.115 -0.0517 0.2778 0.0745 0.2252 27.9997 39.9834 106.9309 14 4.3886 2.641 0.1764 2.8013 -0.8362 0.74 -0.4172 -0.808 0.4291 0.0774 -0.0349 -0.294 -0.2726 -0.3809 0.4521 0.1439 0.1951 -0.1802 0.3155 -0.287 0.3042 35.1215 60.9782 112.5217 15 0.8617 0.052 0.7457 0.5142 0.0606 0.9286 -0.0847 -0.1499 0.144 -0.1103 0.0316 0.0279 -0.0554 -0.1218 0.0532 0.0787 0 0.0015 0.0413 -0.0311 0.2206 29.9617 54.8929 97.2107 16 1.9001 2.903 -1.576 6.4042 -6.132 8.3649 -0.0274 0.4019 -0.194 0.2206 0.6411 0.1015 -0.4526 -0.4061 -0.6137 0.1373 0.0627 0.0461 0.2533 0.0316 0.1435 30.9521 46.0877 123.5233 17 1.0675 1.1378 0.6132 2.5727 -1.7039 6.917 0.0533 -0.0474 -0.0298 -0.071 -0.0707 0.1436 -0.1669 -0.264 0.0173 0.1176 0.0434 -0.0378 0.1015 -0.0129 0.1244 23.4311 37.675 137.8942 18 2.0302 0.7821 0.2464 0.7813 0.1942 0.1947 0.2566 -0.1901 -0.0563 0.0107 -0.2092 -0.0653 -0.0009 -0.0634 -0.0473 0.0982 -0.0023 -0.0153 0.0661 0.0616 0.2035 35.7964 33.7107 147.4929 19 4.1515 1.0164 -3.7773 4.7335 -0.8976 3.4427 0.1273 0.19 0.2175 0.2149 0.1029 -0.0759 -0.1057 -0.1638 -0.2302 0.1105 0.0662 0.0024 0.0476 -0.0002 0.2056 39.3417 22.1922 134.6044 20 3.065 -0.4113 -0.2414 0.1536 0.4322 1.694 -0.0102 0.2533 -0.2725 0.0681 -0.0715 0.0531 0.1955 -0.1709 0.0817 0.1653 -0.0119 0.021 0.0388 -0.0527 0.187 29.1069 14.6671 134.5818
精密化 TLSグループ 大きな表を表示 (5 x 20) 大きな表を隠す ID Refine-ID Refine TLS-ID Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 A4 - 26 2 X-RAY DIFFRACTION 2 A27 - 31 3 X-RAY DIFFRACTION 3 A32 - 109 4 X-RAY DIFFRACTION 4 A110 - 159 5 X-RAY DIFFRACTION 5 A160 - 179 6 X-RAY DIFFRACTION 6 A202 - 335 7 X-RAY DIFFRACTION 7 A336 - 351 8 X-RAY DIFFRACTION 8 A352 - 419 9 X-RAY DIFFRACTION 9 A420 - 436 10 X-RAY DIFFRACTION 10 A437 - 489 11 X-RAY DIFFRACTION 11 C4 - 26 12 X-RAY DIFFRACTION 12 C27 - 31 13 X-RAY DIFFRACTION 13 C32 - 109 14 X-RAY DIFFRACTION 14 C110 - 154 15 X-RAY DIFFRACTION 15 C155 - 337 16 X-RAY DIFFRACTION 16 C338 - 345 17 X-RAY DIFFRACTION 17 C346 - 357 18 X-RAY DIFFRACTION 18 C358 - 419 19 X-RAY DIFFRACTION 19 C420 - 436 20 X-RAY DIFFRACTION 20 C437 - 489