ソフトウェア 名称 バージョン 分類 SBC-Collectデータ収集 HKL-3000データ収集 HKL-3000位相決定 PHENIXモデル構築 PHENIX(phenix.refine: 1.7.3_920)精密化 HKL-3000データ削減 HKL-3000データスケーリング PHENIX位相決定
精密化 構造決定の手法 : 単波長異常分散 / 解像度 : 2.011→38.845 Å / SU ML : 0.22 / Isotropic thermal model : mixed / 交差検証法 : THROUGHOUT / σ(F) : 0 / 位相誤差 : 22.04 / 立体化学のターゲット値 : MLHLRfactor 反射数 %反射 Selection details Rfree 0.226 1968 8.63 % random Rwork 0.18 - - - all 0.184 22792 - - obs 0.184 22792 91.01 % -
溶媒の処理 減衰半径 : 1.24 Å / VDWプローブ半径 : 1.4 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL / Bsol : 33.898 Å2 / ksol : 0.31 e/Å3 原子変位パラメータ Biso mean : 36.8 Å2 Baniso -1 Baniso -2 Baniso -3 1- 1.116 Å2 -0 Å2 0.9729 Å2 2- - -2.4616 Å2 -0 Å2 3- - - 1.3456 Å2
精密化ステップ サイクル : LAST / 解像度 : 2.011→38.845 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2523 0 11 191 2725
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.013 2732 X-RAY DIFFRACTION f_angle_d1.419 3735 X-RAY DIFFRACTION f_dihedral_angle_d16.055 1058 X-RAY DIFFRACTION f_chiral_restr0.087 441 X-RAY DIFFRACTION f_plane_restr0.006 501
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection obs % reflection obs (%)2.0111-2.0614 0.2953 70 0.2177 753 823 46 2.0614-2.1172 0.2698 99 0.2204 1059 1158 66 2.1172-2.1795 0.2656 127 0.2046 1313 1440 81 2.1795-2.2498 0.2628 141 0.2014 1475 1616 90 2.2498-2.3302 0.26 149 0.1816 1575 1724 97 2.3302-2.4235 0.2275 156 0.1885 1603 1759 98 2.4235-2.5338 0.2188 148 0.19 1594 1742 99 2.5338-2.6673 0.2308 151 0.185 1605 1756 99 2.6673-2.8344 0.2591 154 0.1955 1643 1797 100 2.8344-3.0532 0.2477 155 0.2075 1595 1750 100 3.0532-3.3603 0.2188 154 0.1826 1643 1797 100 3.3603-3.8461 0.2328 154 0.1726 1640 1794 100 3.8461-4.8442 0.2002 154 0.1482 1649 1803 100 4.8442-38.8521 0.1932 156 0.1728 1677 1833 100
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 15) 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 4.4301 -2.2028 0.5919 1.4822 1.1932 5.8165 -0.0011 0.9014 0.4734 -0.6291 0.1948 -0.4266 -0.9399 0.3753 -0.6097 0.653 -0.2002 0.118 0.4111 -0.1018 0.0605 26.0567 44.5992 20.505 2 3.8828 -0.5862 -4.5109 0.2778 0.2368 7.716 -0.0051 -0.3204 0.0788 -0.1821 0.1534 0.0206 0.0635 0.5446 -0.1668 0.2637 -0.0283 0.0244 0.2275 -0.0265 0.2914 13.2209 36.9257 47.1671 3 6.1552 2.0607 -3.3633 5.2844 -0.3053 6.532 -0.0266 0.2436 0.8929 0.0476 0.3019 -0.2487 -0.236 -0.0177 -0.2947 0.2201 0.0579 -0.0522 0.1966 -0.0532 0.3352 6.9086 46.4211 58.9781 4 1.6739 -1.2431 0.2643 5.6812 0.7611 1.8647 -0.1073 -0.0995 0.0187 0.3244 0.0854 0.1927 -0.1416 -0.202 0.0244 0.1786 -0.0147 0.0025 0.2145 0.023 0.1997 -0.2811 48.7226 56.4131 5 6.3793 -2.759 -4.9317 1.2275 2.1721 5.7754 -0.2502 0.9488 -0.8283 -0.3816 -0.2273 0.5365 0.1752 -0.8028 0.2531 0.4031 -0.0668 -0.017 0.3687 -0.055 0.2938 6.5923 34.4472 39.771 6 4.0887 -1.8571 -3.0383 8.4176 1.3098 5.4796 0.1936 0.6629 0.5119 -0.5371 0.4024 0.7407 -0.2188 -1.4588 -0.4173 0.4303 -0.0894 -0.0483 0.5869 0.1261 0.2726 8.7702 39.2779 30.4566 7 4.2977 2.5108 -2.0798 5.8826 -2.8855 6.6234 -0.0317 0.3422 0.1171 0.0054 0.2992 0.4304 -0.105 -0.5777 -0.298 0.203 0.0027 0.0218 0.2306 -0.0122 0.1358 11.9166 41.3012 38.2261 8 5.1842 -2.1569 -0.3581 0.9543 0.8319 8.1507 -0.0009 0.3198 -0.6126 -0.0292 0.343 0.5574 0.6444 -1.2241 -0.1926 0.1057 0.0295 -0.0695 0.4307 0.1659 0.5769 -13.4941 59.665 54.0749 9 8.4253 -0.2276 -3.3005 0.1419 0.3605 2.4317 -0.1053 -0.8162 -0.0508 -0.0756 0.0888 0.1638 -0.0181 0.3223 -0.0205 0.2266 0.0002 0.0375 0.2569 0.0207 0.228 14.9933 67.375 45.6448 10 3.4966 -0.5724 -0.2255 5.1954 0.0192 2.3083 -0.2307 0.0171 -0.3045 0.6217 0.3048 -0.1058 0.2824 -0.0586 -0.0952 0.2826 0.0197 -0.0189 0.2037 -0.0159 0.1293 24.5057 63.5734 40.5024 11 1.8315 -1.7356 -0.2705 8.946 1.8748 1.1781 0.2094 0.3788 -0.1074 -0.2872 -0.4062 0.3793 0.0952 -0.4203 0.0645 0.1995 -0.0247 -0.0124 0.2218 0.0237 0.1113 19.0696 59.5981 32.868 12 2.0924 -0.7732 0.2284 6.7253 -0.0951 1.4583 0.0462 0.1216 -0.1182 -0.2135 0.1259 -0.7327 0.1718 0.2188 -0.1503 0.2761 0.0014 0.0235 0.2752 -0.04 0.2486 30.4661 49.9245 31.9924 13 5.4815 -1.3487 -4.5372 0.708 1.9461 5.621 0.6874 0.8288 0.3717 -0.5915 -0.2107 0.1978 -0.9104 -0.6746 -0.2427 0.329 0.0573 -0.0351 0.3262 0.0619 0.3648 9.1136 69.7243 37.2042 14 6.0919 -1.488 -3.8239 7.1853 2.316 3.4798 -0.2287 1.4021 -0.5865 -0.7408 0.1986 0.8158 0.3055 -0.3342 0.0796 0.2563 -0.0227 -0.0505 0.6404 0.0847 0.3572 -0.8566 64.9242 38.7803 15 6.7811 3.9837 -1.1619 7.0613 -1.5906 4.1981 -0.3004 0.5806 0.0078 -0.6824 0.2605 0.0336 -0.0386 -0.1453 0.0559 0.1878 0.0176 0.0101 0.23 0.0166 0.1797 6.3478 63.0369 42.9922
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 296:311)2 X-RAY DIFFRACTION 2 chain 'A' and (resseq 312:331)3 X-RAY DIFFRACTION 3 chain 'A' and (resseq 332:342)4 X-RAY DIFFRACTION 4 chain 'A' and (resseq 343:405)5 X-RAY DIFFRACTION 5 chain 'A' and (resseq 406:418)6 X-RAY DIFFRACTION 6 chain 'A' and (resseq 419:429)7 X-RAY DIFFRACTION 7 chain 'A' and (resseq 430:458)8 X-RAY DIFFRACTION 8 chain 'B' and (resseq 296:311)9 X-RAY DIFFRACTION 9 chain 'B' and (resseq 312:331)10 X-RAY DIFFRACTION 10 chain 'B' and (resseq 332:355)11 X-RAY DIFFRACTION 11 chain 'B' and (resseq 356:368)12 X-RAY DIFFRACTION 12 chain 'B' and (resseq 369:405)13 X-RAY DIFFRACTION 13 chain 'B' and (resseq 406:418)14 X-RAY DIFFRACTION 14 chain 'B' and (resseq 419:429)15 X-RAY DIFFRACTION 15 chain 'B' and (resseq 430:458)