ソフトウェア 名称 バージョン 分類 XSCALEデータスケーリング MOLREP位相決定 PHENIXdev_2219精密化 PDB_EXTRACT3.15 データ抽出 Cootモデル構築 XDSデータ削減
精密化 構造決定の手法 : 分子置換開始モデル : 4GH5解像度 : 1.55→50 Å / SU ML : 0.14 / 交差検証法 : FREE R-VALUE / σ(F) : 1.36 / 位相誤差 : 15.86 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Selection details Rfree 0.167 2000 1.48 % Random selection Rwork 0.1456 133447 - - obs 0.1459 135447 98.34 % -
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 max : 73.84 Å2 / Biso mean : 17.8481 Å2 / Biso min : 5.27 Å2 精密化ステップ サイクル : final / 解像度 : 1.55→50 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 6882 0 56 1135 8073 Biso mean - - 35.93 32.44 - 残基数 - - - - 969
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.006 7259 X-RAY DIFFRACTION f_angle_d0.767 9894 X-RAY DIFFRACTION f_chiral_restr0.057 1198 X-RAY DIFFRACTION f_plane_restr0.005 1301 X-RAY DIFFRACTION f_dihedral_angle_d11.36 4320
LS精密化 シェル 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)1.55-1.5887 0.2333 140 0.2139 9330 X-RAY DIFFRACTION 97 1.5887-1.6317 0.2014 141 0.1929 9391 X-RAY DIFFRACTION 97 1.6317-1.6797 0.238 141 0.1785 9427 X-RAY DIFFRACTION 97 1.6797-1.7339 0.1889 141 0.1674 9412 X-RAY DIFFRACTION 98 1.7339-1.7959 0.1906 141 0.1573 9435 X-RAY DIFFRACTION 98 1.7959-1.8678 0.1762 142 0.1542 9464 X-RAY DIFFRACTION 98 1.8678-1.9528 0.18 142 0.1543 9502 X-RAY DIFFRACTION 98 1.9528-2.0557 0.1573 143 0.1378 9526 X-RAY DIFFRACTION 98 2.0557-2.1845 0.155 144 0.137 9573 X-RAY DIFFRACTION 99 2.1845-2.3532 0.1699 144 0.1377 9602 X-RAY DIFFRACTION 99 2.3532-2.59 0.1699 144 0.1426 9600 X-RAY DIFFRACTION 99 2.59-2.9647 0.1649 144 0.1432 9645 X-RAY DIFFRACTION 99 2.9647-3.7349 0.1543 146 0.1322 9739 X-RAY DIFFRACTION 100 3.7349-50 0.1419 147 0.1355 9801 X-RAY DIFFRACTION 100
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 24) 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 1.3353 1.0748 1.2065 0.902 1.0234 1.1783 0.0033 -0.073 0.0091 -0.0546 0.0279 -0.0439 -0.1542 0.0393 -0.0544 0.0537 0.0076 -0.0088 0.0597 -0.0014 0.0776 -22.0537 18.4883 24.2922 2 2.3963 -0.0538 1.3866 1.7595 0.2367 1.7893 -0.0102 -0.0301 0.068 -0.0913 0.0104 -0.0067 -0.2462 -0.0178 0.0037 0.0734 0.0057 -0.0053 0.0638 0.0084 0.0709 -26.0984 22.5095 24.2618 3 0.6981 -0.12 0.1873 2.1332 -1.7288 3.1087 -0.0811 -0.0438 0.0821 0.0428 0.0142 0.0444 -0.2041 -0.1834 -0.0072 0.0786 0.0212 -0.0162 0.0897 -0.0126 0.0953 -28.8212 21.5089 30.863 4 1.3585 -0.6135 0.7357 0.8849 -0.3928 1.0721 -0.0689 -0.0296 0.1703 0.0973 -0.0122 -0.0551 -0.0584 0.0012 0.0558 0.0546 -0.007 0.0039 0.0673 -0.0068 0.0982 -18.9436 11.5576 35.9058 5 0.3884 -0.3836 0.0406 0.4692 0.1759 0.6651 -0.0002 0.0013 0.0392 0.0075 0.0175 -0.008 -0.0241 0.0196 -0.0092 0.0447 -0.0094 -0.0017 0.0725 0.0133 0.0924 -19.1318 6.196 29.5358 6 0.9858 -0.1657 0.1384 1.146 0.0767 0.9654 0.0348 0.0019 0.0348 -0.0875 -0.0114 -0.0346 -0.0221 0.0477 -0.0052 0.0539 -0.0069 -0.0028 0.0455 -0.0047 0.0456 -14.2683 5.0775 16.9755 7 1.5034 -0.4 0.244 3.0519 0.5542 1.3562 0.0375 -0.0998 -0.0252 0.108 0.031 0.1718 0.0967 -0.1513 -0.0643 0.0938 0.0141 0.0196 0.0994 0.0429 0.0735 -9.965 -17.3608 52.5126 8 0.2635 -0.3284 0.2648 0.6537 -0.2271 0.5672 -0.0589 -0.0796 -0.0548 0.1113 0.072 0.0575 -0.0203 -0.064 -0.0066 0.0724 0.0109 0.0069 0.0899 0.0142 0.0858 -10.2855 -8.2228 48.1428 9 0.6599 -0.6516 0.2312 1.8904 -0.1359 0.9411 0.1252 -0.3241 -0.0481 0.1793 -0.0725 0.553 -0.0436 -0.4392 0.0146 0.1727 -0.0395 0.0437 0.2562 0.0123 0.2975 -24.7421 -22.3099 36.1416 10 1.483 0.1522 0.5618 1.049 -0.0041 1.4408 0.0575 -0.1103 -0.0351 0.0135 -0.0445 0.0961 0.1424 -0.0706 -0.0009 0.0701 0.0049 0.0075 0.0536 0.0037 0.0882 -8.6097 -19.6634 37.0701 11 1.381 0.4645 0.3186 1.5608 -0.0469 2.4321 0.0065 -0.002 -0.0227 -0.1491 -0.1375 0.1912 -0.0358 -0.3944 0.1617 0.1245 0.0198 -0.0446 0.1359 -0.0524 0.1088 -25.7339 -6.5351 -1.9225 12 0.7401 0.0768 0.6048 1.4099 -0.2049 0.8205 -0.0267 -0.023 0.0465 -0.3074 -0.1995 0.3151 -0.2007 -0.3471 0.0772 0.2215 0.0494 -0.0818 0.159 -0.0598 0.1495 -26.9892 -4.0245 -9.0134 13 0.7203 0.1123 0.4712 2.3282 0.2581 2.3395 0.0271 0.0869 -0.0249 -0.3521 0.0273 0.0054 0.3645 0.2944 -0.0805 0.1771 0.0183 -0.0071 0.1437 -0.0345 0.0795 -12.4929 -15.1988 -8.5957 14 0.3976 0.4606 0.7828 3.2243 -0.9303 2.7938 -0.105 0.1995 -0.0186 -0.4573 0.102 -0.147 -0.1673 0.227 -0.0022 0.1767 -0.0337 0.0132 0.1372 -0.0163 0.1016 -13.2589 -2.2001 -8.4412 15 0.5552 -0.1962 -0.1555 1.3979 -0.7836 1.9284 0.0204 0.0009 -0.1146 -0.0609 0.0126 0.1223 0.1539 -0.0318 -0.0402 0.1059 -0.0043 -0.0197 0.1098 -0.0189 0.1087 -15.5899 -16.6807 6.4375 16 1.6881 0.7608 0.0651 3.6123 -0.4304 1.5482 0.0063 -0.0114 -0.0393 -0.0937 0.0037 -0.0229 -0.016 0.1524 0.0163 0.0562 -0.0017 0.001 0.0721 -0.0087 0.0308 -9.1824 -5.0587 8.8709 17 1.0747 -0.3431 -0.5709 1.6733 -0.5863 0.869 -0.142 0.2077 -0.326 -0.1512 0.0642 0.4574 0.2936 -0.2733 0.047 0.1746 -0.0643 -0.0205 0.1699 -0.0234 0.3133 -31.9394 -13.5382 18.6708 18 0.9445 0.1329 -0.383 1.2322 -0.5361 1.8584 -0.0125 0.0341 -0.0937 -0.0656 -0.0128 0.1135 0.0401 -0.1319 0.0204 0.0663 0.0078 -0.0178 0.0667 -0.025 0.0895 -22.676 -1.6274 12.5675 19 0.7944 0.1576 0.1966 1.7242 -0.7806 0.4458 0.0342 0.0746 -0.0241 -0.1532 -0.0261 -0.1994 0.2626 0.2865 -0.0006 0.1791 0.0858 0.0121 0.1443 -0.0094 0.1417 6.4244 -35.0018 23.7861 20 0.9821 -0.6757 -0.1849 0.8215 -0.3186 0.8348 0.0435 -0.0235 -0.1487 -0.1433 -0.0216 -0.0303 0.404 0.26 -0.0299 0.3018 0.1125 -0.0025 0.177 -0.0232 0.1986 3.5781 -39.3833 17.8465 21 0.5484 -0.6358 0.3828 1.5903 -0.5782 1.1464 0.0764 0.0946 -0.0734 -0.227 -0.1263 -0.1895 0.2694 0.2109 0.0891 0.1557 0.0338 -0.0005 0.1272 -0.0238 0.1299 -2.0939 -26.587 11.5673 22 0.3232 0.3297 0.1048 3.3997 -0.8201 1.228 0.0671 0.0128 -0.0675 -0.033 -0.0052 0.1323 0.1701 0.029 -0.043 0.0836 0.0204 -0.014 0.0781 -0.0075 0.096 -6.5989 -24.5509 19.0227 23 0.342 -0.0291 0.392 1.0704 0.2106 1.1835 0.0057 0.044 -0.0391 -0.1536 -0.0022 -0.0323 0.0383 0.1017 -0.0339 0.0767 0.0175 0.0135 0.0887 0.0121 0.1099 -3.4598 -17.7627 23.7417 24 0.6272 -0.1778 0.2463 1.3674 -0.2011 0.8056 0.01 -0.0084 -0.1279 -0.0137 0.0137 -0.0821 0.1095 0.0424 -0.024 0.0607 0.0159 0.0077 0.0604 0.001 0.0877 -2.5236 -20.8451 31.0869
精密化 TLSグループ 大きな表を表示 (6 x 24) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 9 through 24 )A0 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 25 through 47 )A0 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 48 through 74 )A0 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 75 through 109 )A0 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 110 through 205 )A0 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 206 through 250 )A0 7 X-RAY DIFFRACTION 7 chain 'B' and (resid 8 through 24 )B0 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 25 through 184 )B0 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 185 through 215 )B0 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 216 through 250 )B0 11 X-RAY DIFFRACTION 11 chain 'C' and (resid 9 through 24 )C0 12 X-RAY DIFFRACTION 12 chain 'C' and (resid 25 through 60 )C0 13 X-RAY DIFFRACTION 13 chain 'C' and (resid 61 through 74 )C