ソフトウェア 名称 バージョン 分類 NB MOSFLMデータ削減 Show SCALA3.3.16データスケーリング Show PHASER2.1.4位相決定 Show PHENIX1.8.2_1309精密化 Show PDB_EXTRACT3.11 データ抽出 Show DNAデータ収集
精密化 構造決定の手法 : 分子置換 / 解像度 : 1.699→23.555 Å / Occupancy max : 1 / Occupancy min : 0.23 / SU ML : 0.19 / σ(F) : 0.33 / 位相誤差 : 22.16 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Rfree 0.2084 2375 5.05 % Rwork 0.173 - - obs 0.1748 47066 97.46 % all - 47081 -
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL原子変位パラメータ Biso mean : 13.8974 Å2 Baniso -1 Baniso -2 Baniso -3 1- 2.3496 Å2 -0 Å2 -0.6055 Å2 2- - -1.237 Å2 -0 Å2 3- - - -0.4832 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.699→23.555 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3768 0 58 408 4234
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.007 3959 X-RAY DIFFRACTION f_angle_d1.109 5390 X-RAY DIFFRACTION f_dihedral_angle_d12.057 1431 X-RAY DIFFRACTION f_chiral_restr0.07 604 X-RAY DIFFRACTION f_plane_restr0.006 688
LS精密化 シェル 大きな表を表示 (7 x 17) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.699-1.7334 0.2941 130 0.2294 2325 X-RAY DIFFRACTION 87 1.7334-1.7711 0.2275 142 0.1904 2665 X-RAY DIFFRACTION 100 1.7711-1.8123 0.2382 137 0.1755 2681 X-RAY DIFFRACTION 100 1.8123-1.8576 0.2102 138 0.1707 2663 X-RAY DIFFRACTION 100 1.8576-1.9078 0.2293 153 0.1707 2685 X-RAY DIFFRACTION 99 1.9078-1.9639 0.3024 125 0.2565 2627 X-RAY DIFFRACTION 98 1.9639-2.0273 0.2083 127 0.1672 2680 X-RAY DIFFRACTION 99 2.0273-2.0997 0.1886 132 0.1589 2687 X-RAY DIFFRACTION 99 2.0997-2.1837 0.1992 143 0.1587 2667 X-RAY DIFFRACTION 100 2.1837-2.283 0.3009 134 0.2389 2495 X-RAY DIFFRACTION 93 2.283-2.4033 0.1997 139 0.1657 2681 X-RAY DIFFRACTION 99 2.4033-2.5537 0.2189 157 0.1674 2656 X-RAY DIFFRACTION 99 2.5537-2.7506 0.2013 154 0.1635 2663 X-RAY DIFFRACTION 99 2.7506-3.0269 0.1911 132 0.1655 2648 X-RAY DIFFRACTION 98 3.0269-3.4637 0.1831 164 0.1556 2635 X-RAY DIFFRACTION 98 3.4637-4.3593 0.1525 125 0.1457 2652 X-RAY DIFFRACTION 97 4.3593-23.5574 0.1906 143 0.1638 2581 X-RAY DIFFRACTION 93
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 14) 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 2.2699 1.2861 -0.7869 1.9442 -0.5707 0.9228 -0.1006 0.0555 -0.1902 -0.1754 0.0183 -0.2346 0.1332 0.0815 0.0777 0.0728 0.0043 0.01 0.0615 0.0049 0.0661 7.3223 -5.231 25.8152 2 1.0415 -0.3518 -0.5045 1.5961 0.234 1.5838 0.0354 0.2062 0.0104 -0.174 -0.009 0.1207 0.0413 -0.1222 -0.0206 0.0605 -0.0021 -0.0151 0.0701 0.0049 0.0452 -4.0375 0.4062 24.7946 3 1.7487 0.8817 -2.1278 0.693 -0.5553 3.5024 0.1258 0.0129 0.1433 -0.0045 0.0666 -0.007 -0.4257 0.183 -0.119 0.1516 -0.0343 0.0007 0.1116 0.0025 0.1251 15.4699 8.1375 32.543 4 5.368 -0.5315 -1.3115 1.3531 -0.0178 1.3182 0.1004 0.2161 0.4926 -0.2217 -0.0288 -0.0599 -0.1898 0.0257 -0.0221 0.1199 -0.015 0.0065 0.0779 0.032 0.0865 3.6085 12.8567 22.1151 5 3.1354 -0.2136 0.596 1.2881 -0.3016 0.9888 0.0213 -0.1804 0.1002 0.1424 -0.041 0.0816 -0.0458 -0.0914 0.024 0.0746 -0.0032 0.0076 0.0499 -0.0058 0.0308 -5.8109 6.7135 37.4684 6 9.4584 3.8249 4.131 2.4616 1.0374 2.5137 0.2304 -0.5074 0.0227 0.2129 -0.2546 0.1759 0.0256 -0.2043 0.0289 0.1413 -0.0211 0.022 0.0748 0.012 0.0685 -5.5485 -6.2125 41.43 7 4.9357 3.7923 -4.6452 4.9775 -2.8913 7.0141 -0.1769 0.2441 -0.1972 -0.1193 0.1317 -0.1839 0.1103 0.1104 -0.0646 0.1061 0.0288 0.0483 0.1052 -0.0298 0.1792 30.27 -3.7421 56.022 8 2.2807 1.1031 -0.396 2.1923 -0.4305 1.0535 -0.043 0.1903 -0.1427 -0.0958 0.0019 -0.1818 0.1144 0.043 0.0436 0.0618 0.008 0.0064 0.0631 -0.004 0.0436 19.7787 -4.8482 62.3438 9 2.5701 2.7641 0.0642 8.9545 -0.6169 2.3658 -0.0681 0.2118 -0.0049 -0.3332 -0.0132 0.2779 0.0455 -0.1383 0.0251 0.0774 0.0101 -0.0181 0.1167 -0.0156 0.0391 11.3929 -4.4922 54.7917 10 0.8838 -0.7575 -0.6898 1.0996 -0.2829 1.6013 0.0601 0.1744 0.1924 -0.0333 -0.0063 -0.0021 -0.0809 -0.064 -0.0264 0.0598 0.0033 -0.016 0.0655 0.0177 0.0633 12.441 5.6675 63.2271 11 1.8962 -0.1584 -3.4295 -0.0015 0.2778 6.1604 0.2098 -0.1129 -0.0479 0.2034 0.0684 -0.3278 -0.0155 0.4706 -0.2243 0.1447 -0.0396 -0.0617 0.1952 -0.0138 0.1648 29.2605 3.43 72.9829 12 6.2105 0.3782 -1.9723 1.6703 -0.4448 1.6057 0.1177 0.355 0.5069 -0.1642 0.0206 -0.001 -0.1974 -0.1068 -0.1093 0.1394 0.0123 0.0036 0.0693 0.0314 0.0842 14.4652 12.8493 58.8413 13 2.4165 -0.3985 0.5605 1.0199 -0.4895 1.4604 0.0345 -0.1101 0.0505 0.1493 -0.0002 0.1269 -0.0881 -0.0527 -0.0359 0.0861 -0.0043 0.0093 0.0352 -0.0103 0.0542 9.6367 6.4441 74.8941 14 2.1152 3.0143 5.2514 2.7767 0.6308 4.2695 0.0034 -0.596 0.1833 0.3006 -0.1059 0.3201 0.1435 -0.3706 0.0019 0.1062 -0.0099 0.0352 0.1056 -0.0242 0.091 8.7607 -6.4541 76.6927
精密化 TLSグループ ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resseq 2:69)2 X-RAY DIFFRACTION 2 chain 'A' and (resseq 70:131)3 X-RAY DIFFRACTION 3 chain 'A' and (resseq 132:160)4 X-RAY DIFFRACTION 4 chain 'A' and (resseq 161:179)5 X-RAY DIFFRACTION 5 chain 'A' and (resseq 180:231)6 X-RAY DIFFRACTION 6 chain 'A' and (resseq 232:250)7 X-RAY DIFFRACTION 7 chain 'B' and (resseq 2:13)8 X-RAY DIFFRACTION 8 chain 'B' and (resseq 14:69)9 X-RAY DIFFRACTION 9 chain 'B' and (resseq 70:89)10 X-RAY DIFFRACTION 10 chain 'B' and (resseq 90:143)11 X-RAY DIFFRACTION 11 chain 'B' and (resseq 144:160)12 X-RAY DIFFRACTION 12 chain 'B' and (resseq 161:183)13 X-RAY DIFFRACTION 13 chain 'B' and (resseq 184:231)14 X-RAY DIFFRACTION 14 chain 'B' and (resseq 232:250)