ソフトウェア 名称 バージョン 分類 NB SCALEPACKデータスケーリング Show PHASER2.1.4位相決定 Show PHENIX1.7.3_928精密化 Show PDB_EXTRACT3.1 データ抽出 Show ADSCQuantumデータ収集 DENZOデータ削減
精密化 構造決定の手法 : 分子置換開始モデル : PDB ENTRY 3I82解像度 : 1.998→59.595 Å / Occupancy max : 1 / Occupancy min : 0.27 / SU ML : 0.2 / 交差検証法 : THROUGHOUT / σ(F) : 1.34 / 位相誤差 : 16.28 / 立体化学のターゲット値 : MLHL詳細 : REFINEMENT WAS CARRIED OUT WITH EXPLICIT HYDROGENS AS DEFINED BY THE RIDING MODEL.Rfactor 反射数 %反射 Selection details Rfree 0.193 3311 5.08 % RANDOM Rwork 0.1703 - - - obs 0.1715 65223 98.63 % -
溶媒の処理 減衰半径 : 0.98 Å / VDWプローブ半径 : 1.2 Å / 溶媒モデル : FLAT BULK SOLVENT MODEL / Bsol : 40.001 Å2 / ksol : 0.4 e/Å3 原子変位パラメータ Biso max : 105.6 Å2 / Biso mean : 33.5746 Å2 / Biso min : 15.06 Å2 Baniso -1 Baniso -2 Baniso -3 1- 2.3459 Å2 0 Å2 -0 Å2 2- - 2.3459 Å2 -0 Å2 3- - - -4.6918 Å2
精密化ステップ サイクル : LAST / 解像度 : 1.998→59.595 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 4824 0 1 245 5070
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.007 5003 X-RAY DIFFRACTION f_angle_d1.058 6827 X-RAY DIFFRACTION f_chiral_restr0.065 801 X-RAY DIFFRACTION f_plane_restr0.005 901 X-RAY DIFFRACTION f_dihedral_angle_d13.036 1809
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 24
大きな表を表示 (7 x 24) 大きな表を隠す 解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)1.998-2.0266 0.2209 128 0.1879 2490 2618 98 2.0266-2.0569 0.211 130 0.1731 2582 2712 100 2.0569-2.089 0.2044 141 0.1774 2541 2682 100 2.089-2.1233 0.2088 135 0.1672 2604 2739 100 2.1233-2.1599 0.1861 139 0.1635 2545 2684 100 2.1599-2.1992 0.1782 129 0.1615 2582 2711 100 2.1992-2.2415 0.1828 136 0.1594 2560 2696 99 2.2415-2.2872 0.1723 148 0.1601 2579 2727 99 2.2872-2.3369 0.1775 129 0.1544 2564 2693 99 2.3369-2.3913 0.1869 132 0.1609 2552 2684 100 2.3913-2.4511 0.2135 128 0.1624 2580 2708 99 2.4511-2.5174 0.185 144 0.1674 2576 2720 100 2.5174-2.5915 0.1739 167 0.1619 2555 2722 100 2.5915-2.6751 0.1922 133 0.1628 2589 2722 100 2.6751-2.7707 0.1943 133 0.159 2613 2746 100 2.7707-2.8817 0.1852 155 0.1622 2586 2741 100 2.8817-3.0128 0.1879 115 0.1671 2618 2733 99 3.0128-3.1716 0.2106 140 0.168 2597 2737 100 3.1716-3.3703 0.1989 125 0.1811 2637 2762 99 3.3703-3.6305 0.2207 145 0.1782 2608 2753 98 3.6305-3.9958 0.1958 147 0.1705 2562 2709 97 3.9958-4.5738 0.1565 137 0.1534 2551 2688 95 4.5738-5.7618 0.197 156 0.1682 2524 2680 93 5.7618-59.6215 0.2055 139 0.2112 2717 2856 94
精密化 TLS 手法 : refined / Refine-ID : X-RAY DIFFRACTION
大きな表を表示 (25 x 26) 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 1.2538 -1.1989 0.6014 3.376 -1.5127 1.6049 0.0811 0.0255 -0.0857 0.0075 -0.1232 -0.6863 0.0606 0.468 0.1746 0.1207 0.0135 -0.0534 0.2919 0.044 0.2888 -29.7694 -2.8977 1.5896 2 7.1649 5.7528 -0.0526 4.6828 0.6121 6.5989 -0.2797 0.3549 -0.4209 0.0657 0.0468 -0.4738 -0.3576 -0.3958 0.1497 0.2234 0.0394 -0.0788 0.2487 -0.072 0.3641 -48.1389 19.1044 -2.7976 3 5.1393 -2.7613 0.4915 2.2079 0.4825 1.7071 -0.3096 -0.3213 0.1105 0.5686 0.081 0.3327 -0.0831 -0.0709 0.1654 0.1847 -0.0239 0.0216 0.2238 -0.002 0.2569 -43.4581 11.8797 2.9649 4 1.9189 -0.3492 -1.1488 2.3553 1.8302 5.38 0.0037 -0.1692 0.1085 0.2333 -0.0414 -0.0106 0.1672 0.1836 0.0478 0.0904 -0.0239 -0.0128 0.1473 0.0069 0.1906 -39.985 1.6293 1.1305 5 0.6269 0.5142 0.7236 6.6365 1.4329 1.5181 -0.017 -0.0966 0.0488 0.5072 -0.0644 -0.3611 -0.0424 0.1467 0.0779 0.1712 -0.0213 0.0006 0.2427 0.0233 0.212 -34.788 4.1582 6.9834 6 4.0989 -0.8439 -1.9853 2.49 0.77 3.5466 -0.005 -0.4265 -0.14 0.371 0.1508 -0.2456 0.2145 0.5565 -0.245 0.1603 0.0083 -0.0671 0.2185 0.0278 0.1843 -36.4899 -11.7749 8.0462 7 5.7544 -0.8909 -0.8031 9.1066 0.3707 7.0517 -0.1315 -0.1497 0.0105 0.0394 -0.2025 0.1426 0.4341 -1.0234 0.2938 0.262 -0.0804 0.0506 0.3135 -0.0924 0.2542 -49.6282 -0.5384 14.6121 8 2.5023 0.4682 -0.6838 2.7385 -0.8179 7.1543 0.1825 -0.2933 -0.1498 0.4515 -0.0653 -0.051 0.2309 -0.0565 -0.085 0.2053 -0.0375 -0.0113 0.1742 0.0184 0.1417 -47.4587 -16.0329 8.9992 9 2.2085 -0.3601 -0.7496 1.9818 0.7057 3.728 0.0338 -0.3463 -0.2282 0.5251 -0.0008 -0.1758 0.2046 0.2851 -0.0389 0.2438 -0.0151 -0.0464 0.1829 0.0373 0.2055 -42.4779 -16.8289 7.76 10 1.665 0.0772 -0.0125 1.6571 1.6949 5.058 0.1726 -0.2504 -0.1752 -0.0778 -0.0509 -0.1658 0.1283 -0.11 -0.2027 0.2495 0.0408 0.0004 0.1731 0.0288 0.227 -48.5348 -25.2494 -6.7792 11 1.7243 0.7457 0.5796 2.4411 -0.1606 1.8885 -0.0072 -0.1982 -0.1133 -0.032 0.0033 0.1068 0.1855 -0.2453 -0.0326 0.1166 0.0306 0.0055 0.1322 0.0131 0.101 -53.1123 -22.6997 -6.3466 12 2.5553 0.7327 -0.6591 4.4723 -1.1006 5.4291 0.1536 -0.3343 -0.451 0.0365 -0.1076 -0.0794 0.6141 -0.2658 -0.0147 0.2052 -0.0224 -0.0557 0.2275 0.0697 0.2536 -54.0221 -32.0337 -4.2673 13 7.5877 2.3419 -0.2032 4.8218 -0.2045 1.1952 -0.2925 0.4407 -0.1908 -0.6199 0.212 -0.2096 0.5134 -0.0868 0.1301 0.3609 0.0304 0.0354 0.1832 -0.0153 0.1609 -48.0594 -23.5806 -25.9772 14 1.3109 1.4014 -0.5545 2.4308 -0.9249 2.7269 -0.0319 0.1308 0.066 -0.348 0.2364 0.3172 0.3911 -0.3134 -0.2148 0.2552 -0.0266 -0.0574 0.1846 0.0367 0.1989 -62.191 -19.4452 -21.9387 15 2.3921 1.1814 2.4942 1.8083 3.6038 7.2258 0.2166 0.0183 -0.0519 -0.4674 -0.0548 0.6453 0.9947 -0.9569 -0.4361 0.3451 -0.073 -0.1325 0.2054 0.1045 0.2275 -65.2905 -15.7595 -23.594 16 2.9882 0.2272 0.1035 1.6614 -0.1862 0.7849 -0.0233 0.1508 -0.0504 -0.1003 0.0965 0.124 0.293 -0.134 -0.0797 0.1768 -0.0208 -0.0065 0.124 0.0327 0.0883 -56.496 -14.2486 -20.3978 17 2.5889 1.0731 -0.3564 1.1661 -1.1772 1.5968 0.0911 0.1542 -0.5132 -0.3379 0.0057 -0.2188 0.7166 -0.0549 -0.0716 0.5064 -0.0283 0.0034 0.2126 -0.0299 0.1227 -55.0432 -17.8408 -34.5013 18 5.4321 2.3415 1.0931 3.5211 0.2058 2.7417 -0.2875 0.2594 -0.0524 -0.4167 0.1202 0.0717 0.0109 0.2384 0.1547 0.2593 0.0351 0.0226 0.1122 0.0516 0.1141 -49.3814 -1.1834 -29.8796 19 2.5891 -0.7893 1.431 1.9973 -0.7096 2.3966 -0.0816 0.1604 0.1911 -0.2166 -0.0682 0.0753 -0.1057 -0.0039 0.1464 0.1825 0.0045 0.0108 0.1373 0.0135 0.1364 -53.1161 1.6636 -29.5446 20 4.3525 -0.5876 -1.8442 1.9026 1.3788 2.3164 -0.264 0.3611 0.3968 -0.2018 -0.1529 -0.2987 -0.3662 0.5487 0.2839 0.2415 -0.0708 -0.0012 0.2641 0.1068 0.2594 -37.8389 11.2648 -23.0755 21 0.1529 -0.0769 -0.7807 4.8753 0.0268 4.0787 -0.2615 0.1747 0.3377 0.0889 -0.4006 0.7524 -0.9838 -0.8015 0.0242 0.3429 0.0916 -0.1886 0.2276 -0.1222 0.4717 -57.6956 16.2243 -23.4407 22 0.6984 0.1185 -0.5702 3.448 -0.9962 2.3888 -0.234 -0.0151 0.1545 0.2723 -0.0967 0.0876 -0.5559 0.3307 0.3172 0.225 -0.0612 -0.0652 0.1742 0.0344 0.2647 -41.6641 14.8939 -11.4928 23 0.8034 0.2736 -1.0174 2.5214 -0.6144 1.3368 0.0815 -0.0552 0.7456 0.2478 -0.4926 0.7427 -0.7915 -0.2276 0.2033 0.37 0.053 -0.1354 0.1972 -0.0664 0.4577 -50.0428 18.3622 -12.7234 24 1.0155 -0.9155 -0.2359 6.6823 -0.3379 1.3846 -0.094 -0.0437 0.3609 -0.46 -0.0597 0.2302 -0.1407 -0.0757 0.1539 0.1836 -0.0117 -0.067 0.1784 0.0017 0.2296 -46.4604 9.0223 -14.0085 25 4.5502 -2.9102 0.6874 6.1221 -1.1515 2.1494 -0.2794 0.3433 0.7763 -0.308 -0.2534 -0.2047 -0.5501 0.4596 0.3335 0.3522 -0.1448 -0.1076 0.261 0.0756 0.316 -37.3376 19.6918 -16.3945 26 3.1876 1.2829 3.4969 1.5371 3.0132 6.3551 0.1307 0.18 -0.0572 -0.0368 0.1843 -0.3592 -0.3609 1.0204 -0.2622 0.1789 -0.081 -0.0447 0.3275 0.0391 0.3383 -25.004 12.1013 4.4116
精密化 TLSグループ 大きな表を表示 (6 x 26) 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 (resseq 1:16)A1 - 16 2 X-RAY DIFFRACTION 2 chain 'A' and (resseq 17:27)A17 - 27 3 X-RAY DIFFRACTION 3 chain 'A' and (resseq 28:43)A28 - 43 4 X-RAY DIFFRACTION 4 chain 'A' and (resseq 44:82)A44 - 82 5 X-RAY DIFFRACTION 5 chain 'A' and (resseq 83:116)A83 - 116 6 X-RAY DIFFRACTION 6 chain 'A' and (resseq 117:132)A117 - 132 7 X-RAY DIFFRACTION 7 chain 'A' and (resseq 133:146)A133 - 146 8 X-RAY DIFFRACTION 8 chain 'A' and (resseq 147:176)A147 - 176 9 X-RAY DIFFRACTION 9 chain 'A' and (resseq 177:215)A177 - 215 10 X-RAY DIFFRACTION 10 chain 'B' and (resseq 1:26)B1 - 26 11 X-RAY DIFFRACTION 11 chain 'B' and (resseq 27:82)B27 - 82 12 X-RAY DIFFRACTION 12 chain 'B' and (resseq 83:106)B83 - 106 13 X-RAY DIFFRACTION 13 chain 'B' and (resseq 107:128)B107 - 128 14 X-RAY DIFFRACTION 14 chain 'B' and (resseq 129:166)B129 - 166 15 X-RAY DIFFRACTION 15 chain 'B' and (