ソフトウェア 名称 バージョン 分類 Aimless0.7.3データスケーリング PHASER2.8.2位相決定 PHENIX1.14_3260精密化 PDB_EXTRACT3.25 データ抽出 Aimless0.7.3データ削減
精密化 構造決定の手法 : 分子置換開始モデル : JSC1_58120g3 with 18-1,18-2 DHBV-adduct
解像度 : 2.3→36.928 Å / SU ML : 0.39 / 交差検証法 : THROUGHOUT / σ(F) : 1.98 / 位相誤差 : 33.09 Rfactor 反射数 %反射 Rfree 0.2644 638 4.86 % Rwork 0.231 - - obs 0.2326 12858 88.86 %
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 : 124.09 Å2 / Biso mean : 44.266 Å2 / Biso min : 11.93 Å2 精密化ステップ サイクル : final / 解像度 : 2.3→36.928 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 2890 0 90 65 3045 Biso mean - - 34.59 37.96 - 残基数 - - - - 354
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.003 3051 X-RAY DIFFRACTION f_angle_d0.784 4134 X-RAY DIFFRACTION f_dihedral_angle_d13.584 1769 X-RAY DIFFRACTION f_chiral_restr0.048 422 X-RAY DIFFRACTION f_plane_restr0.004 536
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID 数 Refine-ID Rms タイプ 1 1 A1748 X-RAY DIFFRACTION 4.795 TORSIONAL1 2 B1748 X-RAY DIFFRACTION 4.795 TORSIONAL
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork % reflection obs (%)2.3001-2.4777 0.3965 113 0.305 2553 90 2.4777-2.7269 0.3395 105 0.2823 2606 92 2.7269-3.1213 0.3221 143 0.2505 2366 85 3.1213-3.9318 0.2728 149 0.2146 2441 87 3.9318-36.928 0.1991 128 0.2054 2525 90
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 3.6522 -1.9079 0.717 6.6224 -3.7758 8.7211 0.4862 0.4014 0.3282 -1.7558 -1.2224 -0.5962 0.7963 -0.3804 0.5283 0.6569 0.1433 0.1202 0.6375 -0.1856 0.6892 -7.2347 -9.3264 5.286 2 4.6799 1.755 -2.2766 5.829 -1.4001 6.7723 -0.1762 0.6526 -0.2801 -0.306 0.4466 -0.2479 0.4357 -0.1396 -0.2758 0.2067 -0.0029 -0.0485 0.3107 -0.0348 0.3892 -17.0419 -2.8005 8.8452 3 2.934 -1.6917 -0.0723 5.1025 -1.3983 3.5993 -0.0479 -0.1006 0.0939 0.2 0.0178 0.2294 -0.4964 -0.2928 0.0546 0.2692 -0.0265 0.0924 0.2549 -0.0215 0.3097 -18.7135 8.1696 19.5227 4 8.4912 -0.4331 -1.5581 2.376 0.7629 3.651 -0.2196 -0.5965 0.2457 0.1805 0.0564 -0.2574 0.2731 0.2849 0.1612 0.3953 -0.0235 0.019 0.3488 -0.0059 0.2951 -13.2432 -5.2499 31.9167 5 4.2117 -0.5084 3.0781 5.204 -4.4004 5.7725 -0.2909 -1.6794 0.216 0.6811 0.897 -0.0019 -0.1909 -0.7365 -0.4195 0.4727 0.0143 0.0635 0.4667 -0.0286 0.2122 -20.8548 1.087 35.5157 6 1.2282 -0.3266 -0.5969 3.236 0.9145 3.8423 -0.0426 -0.0615 0.1198 0.3029 -0.0034 0.2749 -0.0755 -0.2139 0.0604 0.2089 0.0286 0.004 0.2313 0.0229 0.2349 -18.8962 0.4436 21.1365 7 7.7524 2.5398 -2.1811 4.987 -3.1896 5.1622 -0.1004 0.4705 0.369 0.8292 0.0187 -0.4775 -0.6058 0.0762 0.1033 0.3092 -0.0069 0.0028 0.3438 -0.0228 0.2799 -6.5107 -0.99 13.4209 8 9.5556 5.0493 3.3098 3.3589 2.3428 9.977 0.6972 -1.0077 0.5854 0.8384 -0.4588 0.5563 0.7609 -0.3517 -0.2938 0.7358 0.0365 0.1886 0.6309 0.2804 0.8137 -27.5898 -26.3923 -0.9214 9 2.675 -2.5076 -2.1364 8.2504 1.3712 2.5562 0.1771 -0.973 0.0707 1.1667 0.3369 -0.3394 0.688 0.274 -0.7123 0.4673 0.0448 -0.0376 0.4798 0.0079 0.3677 -19.2592 -21.0616 -2.3276 10 3.8447 0.7699 0.7962 4.31 -0.0733 5.034 -0.0229 -0.3421 0.2301 0.3441 -0.0282 -0.1758 -0.3675 0.0954 0.0934 0.3637 -0.0235 0.0529 0.224 -0.0079 0.3506 -15.75 -13.8183 -11.5522 11 3.3381 -0.6688 -0.213 4.3357 -0.6784 3.9941 0.1709 0.4584 -0.3497 -0.1741 0.0316 -0.318 -0.5424 0.7894 -0.1354 0.3419 -0.0327 0.0228 0.3025 -0.0612 0.3873 -15.8695 -9.733 -18.4798 12 4.5005 0.1325 -0.4907 2.9232 1.7284 5.6321 0.2493 0.9771 -0.6129 -0.348 -0.2748 -0.064 0.2472 -0.5382 0.0802 0.3437 0.0193 -0.0069 0.3564 -0.0389 0.3297 -22.2589 -22.2963 -28.6663 13 0.339 0.3191 -0.3472 2.4929 0.6665 4.3086 -0.0477 0.1536 -0.0568 -0.0899 0.1467 -0.247 -0.2179 0.5326 -0.1257 0.2196 -0.0374 -0.009 0.2958 0.0077 0.3509 -15.7219 -17.0101 -19.1578 14 6.9308 -2.2183 -2.6973 9.4834 6.8757 9.6948 0.423 0.1503 0.5054 -0.1811 -0.6879 0.1634 -0.156 -0.6965 0.2936 0.2714 -0 -0.0255 0.4302 0.0223 0.3131 -28.668 -18.918 -9.9782
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 523:534)A523 - 534 2 X-RAY DIFFRACTION 2 (chain A and resid 535:562)A535 - 562 3 X-RAY DIFFRACTION 3 (chain A and resid 563:605)A563 - 605 4 X-RAY DIFFRACTION 4 (chain A and resid 606:628)A606 - 628 5 X-RAY DIFFRACTION 5 (chain A and resid 629:636)A629 - 636 6 X-RAY DIFFRACTION 6 (chain A and resid 637:675)A637 - 675 7 X-RAY DIFFRACTION 7 (chain A and resid 676:699)A676 - 699 8 X-RAY DIFFRACTION 8 (chain B and resid 523:536)B523 - 536 9 X-RAY DIFFRACTION 9 (chain B and resid 537:551)B537 - 551 10 X-RAY DIFFRACTION 10 (chain B and resid 552:577)B552 - 577 11 X-RAY DIFFRACTION 11 (chain B and resid 578:603)B578 - 603 12 X-RAY DIFFRACTION 12 (chain B and resid 604:631)B604 - 631 13 X-RAY DIFFRACTION 13 (chain B and resid 632:675)B632 - 675 14 X-RAY DIFFRACTION 14 (chain B and resid 676:699)B676 - 699