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 PHENIX(1.15rc1_3423)精密化 PDB_EXTRACT3.24 データ抽出 PHASER位相決定 PARROT位相決定 Cootモデル構築
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 1.7→40.122 Å / SU ML : 0.21 / 交差検証法 : THROUGHOUT / σ(F) : 2.01 / 位相誤差 : 21.76 Rfactor 反射数 %反射 Selection details Rfree 0.2079 1941 6.19 % 0 Rwork 0.1756 - - - obs 0.1775 31339 99.83 % -
溶媒の処理 減衰半径 : 0.9 Å / VDWプローブ半径 : 1.11 Å原子変位パラメータ Biso max : 116.99 Å2 / Biso mean : 46.3919 Å2 / Biso min : 18.09 Å2 精密化ステップ サイクル : final / 解像度 : 1.7→40.122 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 1849 0 8 168 2025 Biso mean - - 37.97 46.25 - 残基数 - - - - 237
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.008 1935 X-RAY DIFFRACTION f_angle_d0.872 2631 X-RAY DIFFRACTION f_dihedral_angle_d15.537 1165 X-RAY DIFFRACTION f_chiral_restr0.064 300 X-RAY DIFFRACTION f_plane_restr0.005 336
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 (%)1.7002-1.7427 0.3265 126 0.2664 2153 2279 100 1.7427-1.7898 0.2747 158 0.2374 2067 2225 100 1.7898-1.8425 0.2357 157 0.2153 2078 2235 100 1.8425-1.9019 0.2293 148 0.1978 2092 2240 100 1.9019-1.9699 0.2367 141 0.1957 2095 2236 100 1.9699-2.0488 0.2283 168 0.1881 2065 2233 100 2.0488-2.142 0.2171 130 0.1888 2125 2255 100 2.142-2.255 0.244 96 0.1824 2143 2239 100 2.255-2.3962 0.2348 173 0.1867 2066 2239 100 2.3962-2.5812 0.2262 138 0.1929 2100 2238 100 2.5812-2.8409 0.2359 136 0.1826 2116 2252 100 2.8409-3.2518 0.205 126 0.1774 2094 2220 100 3.2518-4.0963 0.144 109 0.1532 2120 2229 100 4.0963-40.1336 0.1997 135 0.1583 2084 2219 99
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 3.5165 2.8622 -0.6806 2.6412 -2.0598 9.2485 -0.0898 -0.0887 -0.3522 -0.4312 -0.4367 -1.0704 0.8923 1.1441 0.5511 0.2907 0.0985 0.0347 0.4334 0.0636 0.3694 67.0803 18.7916 14.5901 2 8.5894 2.1453 2.9347 0.537 0.6476 8.1756 0.61 1.0133 0.2446 -0.468 0.4088 -0.3082 -0.9535 2.0156 -0.2285 0.6039 -0.0109 0.2819 0.7467 0.1296 0.6578 71.7301 25.3969 6.222 3 3.6837 -0.8226 0.3886 6.4494 1.6464 2.4566 -0.0317 -0.6375 -0.0463 0.5006 0.1964 -0.2436 0.3431 0.767 -0.0559 0.3049 0.0734 -0.0288 0.5386 0.1279 0.2868 68.3599 18.945 19.084 4 4.5905 2.0857 0.154 3.2659 3.215 7.1102 -0.068 -0.0146 0.0461 -0.3399 -0.0881 -0.5944 -0.1978 0.8772 0.1012 0.2155 -0.0209 0.008 0.374 0.076 0.2488 65.3555 25.2692 13.3244 5 4.1518 -0.3441 2.1257 7.1982 2.8005 3.6295 0.0911 1.1539 -0.7346 0.1184 -0.3435 0.2037 1.4432 0.1839 -0.161 0.6857 0.1177 0.0936 0.478 -0.1266 0.5893 59.7885 5.6069 5.3468 6 4.69 -4.4933 -4.4132 5.8226 4.1151 4.3115 0.221 0.3263 -0.206 -0.2763 -0.2328 0.3056 -0.0527 -0.4337 0.0315 0.2707 -0.0308 0.0244 0.2522 -0.0449 0.2963 50.8983 21.9547 15.5049 7 7.6987 -4.8813 -4.2341 8.9516 4.8464 3.2444 0.0293 0.9285 -0.4912 -0.5109 -0.5412 0.6693 0.0129 -0.3901 0.6828 0.2294 -0.0216 -0.0263 0.2925 -0.0532 0.2386 50.3593 20.8468 11.0371 8 4.8257 -3.8762 -5.879 3.9205 5.4255 8.5172 -0.0292 0.097 -0.369 -0.0264 -0.0748 0.0915 0.4337 -0.5123 0.0484 0.5371 0.09 0.1401 0.2574 -0.0284 0.3712 65.1053 8.7027 2.6838 9 4.9524 -1.4948 -1.1071 7.4764 -0.5141 5.8868 -0.1252 -0.0967 -0.3714 0.1365 -0.1848 0.3467 0.4731 0.3084 0.1717 0.2075 -0.0134 0.0325 0.1963 0.0013 0.1829 57.5949 19.6963 14.5561 10 8.3572 2.1115 -1.7127 3.2291 1.8779 4.7576 -1.2921 -0.1024 -1.0246 -0.1283 0.1479 0.3102 0.7275 0.1821 0.8445 1.5348 0.0596 -0.0936 0.8212 -0.0549 1.0012 61.442 35.646 29.344 11 8.7221 0.1616 0.8953 3.8747 -2.1428 5.4547 0.1993 -0.1622 -0.5626 -0.3211 0.1392 0.4116 1.2326 -1.165 -0.2043 0.3945 -0.1589 -0.0502 0.4467 0.0783 0.3274 32.997 17.5978 30.5888 12 5.5983 1.2995 1.334 2.966 -0.9305 4.4855 -0.1949 0.1281 0.3165 -0.2511 0.2678 0.3287 0.1395 -0.6119 0.0042 0.1658 -0.0169 -0.0052 0.2641 0.0342 0.2049 36.6772 26.6091 28.8766 13 8.324 2.5672 3.4017 1.8926 0.6891 3.6219 -0.4624 0.5889 0.567 -0.3422 0.3031 0.3838 -0.2774 -0.3002 0.1808 0.2256 -0.0096 -0.055 0.372 0.0501 0.3048 36.0203 31.0288 25.4567 14 7.1299 0.6261 1.0787 3.8869 -0.771 7.135 -0.1162 -0.1698 0.0588 0.0713 0.144 0.0507 0.1184 -0.4924 -0.0306 0.1295 -0.0187 0.0141 0.1777 0.0036 0.156 39.0252 26.5082 31.6184
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 33 through 41 )A33 - 41 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 42 through 58 )A42 - 58 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 59 through 66 )A59 - 66 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 67 through 79 )A67 - 79 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 80 through 89 )A80 - 89 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 90 through 99 )A90 - 99 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 100 through 109 )A100 - 109 8 X-RAY DIFFRACTION 8 chain 'A' and (resid 110 through 116 )A110 - 116 9 X-RAY DIFFRACTION 9 chain 'A' and (resid 117 through 149 )A117 - 149 10 X-RAY DIFFRACTION 10 chain 'A' and (resid 150 through 168 )A150 - 168 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 33 through 66 )B33 - 66 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 67 through 99 )B67 - 99 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 100 through 116 )B