ソフトウェア 名称 バージョン 分類 XDSデータ削減 XSCALEデータスケーリング PHENIX1.20.1-4487 精密化 PDB_EXTRACT3.27 データ抽出 MoRDa位相決定
精密化 構造決定の手法 : 分子置換開始モデル : 2OI6解像度 : 2.65→49.2 Å / SU ML : 0.37 / 交差検証法 : THROUGHOUT / σ(F) : 1.34 / 位相誤差 : 23.19 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Rfree 0.2043 2009 7.66 % Rwork 0.1688 24230 - obs 0.1715 26239 99.45 %
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.1 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL原子変位パラメータ Biso max : 149.83 Å2 / Biso mean : 73.0274 Å2 / Biso min : 34.04 Å2 精密化ステップ サイクル : final / 解像度 : 2.65→49.2 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 3361 0 27 128 3516 Biso mean - - 95.9 63.3 - 残基数 - - - - 451
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.007 3455 X-RAY DIFFRACTION f_angle_d0.881 4704 X-RAY DIFFRACTION f_chiral_restr0.055 547 X-RAY DIFFRACTION f_plane_restr0.008 629 X-RAY DIFFRACTION f_dihedral_angle_d14.55 1250
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0 / Total num. of bins used : 14
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.65-2.72 0.3562 130 0.3362 1762 1892 100 2.72-2.79 0.3606 159 0.2927 1692 1851 100 2.79-2.87 0.312 158 0.2666 1701 1859 100 2.87-2.96 0.2958 146 0.2337 1714 1860 100 2.96-3.07 0.2892 136 0.2326 1739 1875 100 3.07-3.19 0.2679 127 0.2251 1725 1852 100 3.19-3.34 0.2826 144 0.2262 1740 1884 100 3.34-3.51 0.2288 146 0.1902 1709 1855 100 3.52-3.73 0.1803 151 0.1519 1707 1858 100 3.73-4.02 0.1808 152 0.155 1725 1877 100 4.02-4.42 0.15 134 0.1335 1739 1873 99 4.43-5.07 0.1435 160 0.1169 1741 1901 99 5.07-6.37 0.2179 130 0.1615 1746 1876 99 6.38-49.2 0.178 136 0.1414 1790 1926 97
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 8) 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 4.1808 -1.7309 -2.6915 3.0427 3.0209 5.3021 0.0826 0.1892 0.1122 0.1692 -0.1398 -0.0709 0.2268 -0.325 0.0597 0.435 0.02 -0.0257 0.3955 -0.059 0.5979 -16.7316 17.8152 15.7037 2 4.4895 -1.4092 -0.1552 4.6777 1.8406 6.119 -0.033 0.1701 -0.2793 0.3934 -0.1075 0.3303 0.494 -0.1979 0.1386 0.3561 -0.0017 0.0477 0.2921 -0.023 0.4411 -21.2779 21.6133 23.9681 3 4.1902 1.0122 -0.6909 5.2347 0.2884 6.83 -0.0554 -0.3196 1.1092 0.2724 0.8001 -0.7417 0.1127 1.6661 -0.7152 0.5213 0.1047 -0.1388 0.7817 -0.1973 0.7868 -2.1125 27.5116 32.1113 4 5.1223 -0.9841 2.4244 5.9992 3.2596 6.4557 0.4617 -0.117 0.7383 -0.2291 0.5743 -1.1867 -0.597 1.4388 -1.0286 0.6715 -0.0972 0.1216 0.9545 -0.276 0.9262 0.7254 32.9226 29.0588 5 6.0261 -3.569 0.604 7.1556 2.6298 2.469 -0.2033 0.3215 0.574 -0.1013 -0.0913 -0.2649 -0.4742 0.5923 0.2965 0.6148 -0.0361 -0.0434 0.5311 -0.0468 0.6164 -17.388 35.8273 29.5314 6 0.6258 -1.2707 -1.7761 4.2311 3.1643 1.1113 -0.235 -0.2236 0.0908 0.7012 0.4062 -0.4143 0.3005 0.3491 -0.1796 0.5076 0.087 -0.071 0.4957 -0.0469 0.465 -5.6947 18.8218 23.8687 7 2.9316 0.6872 0.2156 2.9275 -0.2294 2.8409 -0.1115 0.0587 -0.5948 -0.04 0.1097 0.6661 0.5673 -0.5172 0.0177 0.4369 -0.1183 -0.0106 0.4228 0.0132 0.6443 -12.1453 -13.07 4.9505 8 2.3341 0.1698 -0.427 1.5157 -0.1965 1.9011 -0.1221 0.5999 -0.8612 -0.5934 -0.0066 0.5256 0.7547 -0.8241 0.1525 1.0424 -0.4085 -0.3002 1.0735 -0.2415 1.3371 -25.3156 -25.3161 -15.5296
精密化 TLSグループ ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 12 through 53 )A12 - 53 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 54 through 128 )A54 - 128 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 129 through 155 )A129 - 155 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 156 through 180 )A156 - 180 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 181 through 205 )A181 - 205 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 206 through 258 )A206 - 258 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 259 through 390 )A259 - 390 8 X-RAY DIFFRACTION 8 chain 'A' and (resid 391 through 462 )A391 - 462