ソフトウェア 名称 バージョン 分類 PHENIX(1.20.1_4487: ???)精密化 Aimlessデータスケーリング XDSデータ削減 PHASER位相決定
精密化 構造決定の手法 : 分子置換 / 解像度 : 1.55→58.82 Å / SU ML : 0.19 / 交差検証法 : FREE R-VALUE / σ(F) : 1.33 / 位相誤差 : 27.82 / 立体化学のターゲット値 : ML詳細: Lattice-translocation disorder correction notes: Native Patterson shows three off-origin peaks. Strongest one with vector (0.4029 0.50000.618), second one (0.1953 0.000 0.7638), and third one ... 詳細 : Lattice-translocation disorder correction notes: Native Patterson shows three off-origin peaks. Strongest one with vector (0.4029 0.50000.618), second one (0.1953 0.000 0.7638), and third one at (0.2092 0.5000 0.8536), corresponding to 1X Td, 2X Td and 3X Td, respectively, with relative intensities to orgin peak of ~65%, ~30% and 8.5% (CCP4 fft used; phenix.xtriage showed even higher values like 73%, 34% and 10%, most likely due to grid sampling difference), respectively. Peak 1 and 2 are mostly targeted. Peak 1 corresponds to tNCS too, so after correction it is lowered but not eliminated. Peak 2 eventually gone. Final Rwork and Rfee went down to 19.81% and 21.99%,respectively. Without correction, the Rwork and Rfree, with best try, are paused at 31.38% and 33.83%, respectively.Rfactor 反射数 %反射 Rfree 0.2199 5787 5 % Rwork 0.1981 - - obs 0.1992 115703 99.65 %
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精密化ステップ サイクル : LAST / 解像度 : 1.55→58.82 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 5624 0 53 549 6226
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.006 5918 X-RAY DIFFRACTION f_angle_d0.85 8069 X-RAY DIFFRACTION f_dihedral_angle_d12.092 2138 X-RAY DIFFRACTION f_chiral_restr0.053 905 X-RAY DIFFRACTION f_plane_restr0.007 1045
LS精密化 シェル 大きな表を表示 (7 x 30) 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 (%)1.55-1.57 0.3109 218 0.3112 3628 X-RAY DIFFRACTION 100 1.57-1.59 0.3309 200 0.3109 3631 X-RAY DIFFRACTION 100 1.59-1.61 0.3437 185 0.3124 3622 X-RAY DIFFRACTION 100 1.61-1.63 0.3051 199 0.3048 3661 X-RAY DIFFRACTION 99 1.63-1.65 0.3109 183 0.2886 3621 X-RAY DIFFRACTION 100 1.65-1.67 0.2866 215 0.2874 3689 X-RAY DIFFRACTION 100 1.67-1.69 0.2868 194 0.272 3639 X-RAY DIFFRACTION 100 1.69-1.72 0.291 213 0.264 3627 X-RAY DIFFRACTION 100 1.72-1.75 0.3205 187 0.2601 3632 X-RAY DIFFRACTION 100 1.75-1.77 0.2914 186 0.2477 3704 X-RAY DIFFRACTION 100 1.77-1.8 0.255 195 0.2416 3662 X-RAY DIFFRACTION 100 1.8-1.84 0.281 194 0.2281 3606 X-RAY DIFFRACTION 100 1.84-1.87 0.2299 179 0.2254 3711 X-RAY DIFFRACTION 100 1.87-1.91 0.2615 196 0.2216 3651 X-RAY DIFFRACTION 100 1.91-1.95 0.2414 187 0.2187 3635 X-RAY DIFFRACTION 100 1.95-2 0.2438 206 0.2125 3690 X-RAY DIFFRACTION 100 2-2.05 0.2272 194 0.1995 3607 X-RAY DIFFRACTION 100 2.05-2.1 0.217 197 0.1941 3679 X-RAY DIFFRACTION 100 2.1-2.17 0.2264 169 0.1861 3691 X-RAY DIFFRACTION 100 2.17-2.24 0.2139 165 0.1821 3687 X-RAY DIFFRACTION 100 2.24-2.32 0.2165 211 0.178 3675 X-RAY DIFFRACTION 100 2.32-2.41 0.1941 201 0.1769 3666 X-RAY DIFFRACTION 100 2.41-2.52 0.1983 188 0.1758 3671 X-RAY DIFFRACTION 100 2.52-2.65 0.1672 171 0.1712 3676 X-RAY DIFFRACTION 100 2.65-2.82 0.2153 185 0.1798 3685 X-RAY DIFFRACTION 100 2.82-3.03 0.2057 182 0.1821 3700 X-RAY DIFFRACTION 100 3.03-3.34 0.1814 207 0.1751 3691 X-RAY DIFFRACTION 100 3.34-3.82 0.1818 191 0.153 3707 X-RAY DIFFRACTION 100 3.82-4.81 0.1559 204 0.1432 3672 X-RAY DIFFRACTION 100 4.82-58.82 0.2045 185 0.2021 3700 X-RAY DIFFRACTION 98
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 0.2382 0.2615 0.9101 0.5271 0.1738 6.3126 -0.1812 0.0509 0.0952 -0.0529 -0.0902 0.0228 -0.6481 -0.0105 0.2076 0.1961 0.0435 -0.0418 0.1627 -0.0029 0.1929 -11.5253 18.0128 17.2825 2 0.4988 0.1426 0.1441 0.8025 -0.3847 0.8027 -0.0103 0.0094 -0.036 -0.0031 0.0133 -0.0445 0.0916 -0.0099 0.0015 0.1291 0.0249 0.0036 0.1453 -0.0376 0.1214 -1.0876 -7.6486 19.6032 3 1.1638 1.1753 0.8451 4.4704 0.4374 1.3709 -0.0282 -0.0153 -0.1468 -0.0595 0.0711 -0.322 0.0937 0.0986 -0.0389 0.1228 0.031 0.0194 0.1847 -0.0217 0.1178 7.6716 -5.4074 23.6846 4 1.8203 0.2186 0.1626 1.8151 0.6825 1.3086 -0.0915 -0.0176 -0.0452 -0.0808 0.09 -0.0128 -0.0393 0.1543 -0.0027 0.0912 0.0083 0.02 0.1438 -0.0018 0.0638 0.4983 0.776 14.8172 5 1.7929 -0.4663 0.128 3.6362 -0.1524 1.8717 0.0316 0.3949 0.023 -0.2249 0.0361 -0.4488 0.001 0.1417 -0.0797 0.092 0.0003 0.0215 0.1872 -0.0177 0.1566 -10.2612 -5.2709 0.2214 6 2.5085 0.2754 3.5661 0.4515 0.4056 7.3685 -0.1592 0.1042 0.1352 -0.002 0.0423 -0.001 -0.4008 0.2537 0.1132 0.1417 0.0083 -0.0205 0.1098 -0.0338 0.1263 0.4594 15.3077 26.5753 7 2.5598 -0.4744 -1.2319 1.3007 0.4261 3.8103 -0.1644 -0.2778 -0.0858 0.2067 0.0555 -0.0425 0.0104 0.1189 0.0834 0.1363 0.034 -0.0292 0.1404 -0.039 0.1115 2.711 3.858 40.848 8 0.5099 -1.1426 -0.9684 5.0933 2.1267 1.8399 -0.0801 -0.0728 -0.0869 0.0636 -0.0438 0.4919 -0.0037 -0.2051 0.1259 0.103 0.0338 0.0231 0.2135 -0.0254 0.1259 -12.4422 4.8063 41.6831 9 3.232 1.4375 2.5382 3.8994 0.2146 3.0941 0.175 -0.2039 -0.0879 0.0964 -0.1063 0.0194 0.7622 -0.234 -0.0712 0.2595 -0.0253 0.0497 0.1672 0.0127 0.1077 -9.2586 -14.457 35.3968 10 0.9858 0.6969 -0.267 3.9704 0.2962 2.4213 -0.0338 -0.1442 0.1551 0.1134 -0.0217 0.0643 -0.2834 -0.1665 0.06 0.1368 0.0503 -0.0181 0.178 -0.0451 0.1222 -5.2844 13.5888 41.8535 11 0.4707 -0.3777 0.9996 1.0422 0.5186 4.4826 -0.1868 0.0156 0.1157 -0.0328 -0.0127 -0.0758 -0.6115 0.1728 0.1792 0.1248 -0.011 -0.0343 0.1329 -0.021 0.2066 -18.5104 17.831 9.3462 12 0.7945 0.1146 0.1649 0.6109 0.0332 0.8803 -0.0098 -0.0736 -0.046 -0.0077 0.0208 0.0591 0.0204 -0.037 -0.0116 0.0685 0.0103 -0.0002 0.0724 -0.0174 0.103 -28.4875 -7.8484 5.9038 13 1.229 -1.1155 0.6038 3.0965 -1.2276 1.0931 -0.0551 -0.0735 -0.0953 0.0419 0.1222 0.2215 0.0973 -0.1308 -0.0653 0.0736 0.01 0.021 0.095 -0.0365 0.1014 -37.2281 -5.4099 1.9912 14 1.222 0.0413 0.3644 1.1133 -0.4517 1.3077 -0.0271 -0.1403 -0.0145 -0.034 -0.0093 0.0412 -0.0027 -0.126 0.0338 0.0986 0.0296 -0.0043 0.0954 -0.0483 0.1103 -30.0505 0.7637 10.854 15 1.3598 -0.6545 0.372 3.8027 0.2542 0.5687 0.0554 -0.4328 -0.0534 0.3959 -0.0424 0.2753 0.0292 -0.2743 -0.0464 0.1202 -0.0038 0.017 0.2425 -0.0189 0.1141 -19.0825 -4.9989 25.1519 16 0.6179 0.007 1.11 0.4996 0.6285 6.4178 -0.1268 -0.0678 0.1499 -0.0011 -0.0517 0.0866 -0.3007 -0.3506 0.1722 0.1302 0.0204 -0.0249 0.079 -0.0315 0.1395 -30.0704 15.2023 -0.8837 17 2.2386 0.0931 -0.2602 0.9018 -0.1609 2.2322 -0.0293 0.2341 -0.1082 -0.2949 0.0284 0.0474 0.0263 -0.0606 0.0337 0.169 0.0083 -0.0176 0.088 -0.0356 0.096 -32.2221 3.8642 -15.1958 18 0.6815 1.5298 -0.8466 6.2613 -4.1617 5.1176 -0.0257 0.1886 -0.1094 0.0598 -0.0744 -0.366 -0.1144 0.2499 0.1034 0.0905 0.0239 0.0021 0.1617 -0.0135 0.1442 -17.1049 4.8253 -15.9872 19 2.2309 -0.742 2.3372 1.9377 -0.6517 2.6152 0.2005 0.1026 -0.1996 -0.2287 -0.0409 0.0157 0.3178 0.1707 -0.1359 0.1642 0.0294 0.0066 0.141 -0.0689 0.1314 -20.6346 -14.5223 -9.9353 20 1.6908 -0.5065 0.0296 4.5618 1.2164 2.8552 -0.0663 0.1179 0.0653 -0.2527 -0.023 -0.0834 -0.1509 0.0423 0.0816 0.0748 -0.0056 -0.0134 0.0848 -0.0095 0.0825 -24.2816 13.6126 -16.153
精密化 TLSグループ 大きな表を表示 (4 x 20) 大きな表を隠す ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 32 )2 X-RAY DIFFRACTION 2 chain 'A' and (resid 33 through 126 )3 X-RAY DIFFRACTION 3 chain 'A' and (resid 127 through 164 )4 X-RAY DIFFRACTION 4 chain 'A' and (resid 165 through 206 )5 X-RAY DIFFRACTION 5 chain 'A' and (resid 207 through 239 )6 X-RAY DIFFRACTION 6 chain 'A' and (resid 240 through 270 )7 X-RAY DIFFRACTION 7 chain 'A' and (resid 271 through 305 )8 X-RAY DIFFRACTION 8 chain 'A' and (resid 306 through 326 )9 X-RAY DIFFRACTION 9 chain 'A' and (resid 327 through 349 )10 X-RAY DIFFRACTION 10 chain 'A' and (resid 350 through 377 )11 X-RAY DIFFRACTION 11 chain 'B' and (resid 3 through 32 )12 X-RAY DIFFRACTION 12 chain 'B' and (resid 33 through 126 )13 X-RAY DIFFRACTION 13 chain 'B' and (resid 127 through 164 )14 X-RAY DIFFRACTION 14 chain 'B' and (resid 165 through 206 )15 X-RAY DIFFRACTION 15 chain 'B' and (resid 207 through 239 )16 X-RAY DIFFRACTION 16 chain 'B'