ソフトウェア 名称 バージョン 分類 NB XSCALEデータスケーリング Show PHASER2.1.4位相決定 Show PHENIX1.6.2_432精密化 Show PDB_EXTRACT3.1 データ抽出 Show XDSデータスケーリング XDSデータ削減
精密化 構造決定の手法 : 分子置換 / 解像度 : 3.35→46.2 Å / Occupancy max : 1 / Occupancy min : 1 / FOM work R set : 0.7817 / SU ML : 0.43 / σ(F) : 1.99 / 位相誤差 : 28.58 / 立体化学のターゲット値 : MLRfactor 反射数 %反射 Rfree 0.3004 3705 9.95 % Rwork 0.2446 33514 - obs 0.2502 37219 91.18 %
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 / Bsol : 74.407 Å2 / ksol : 0.273 e/Å3 原子変位パラメータ Biso max : 560.78 Å2 / Biso mean : 107.8704 Å2 / Biso min : 3.18 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.196 Å2 0 Å2 -0 Å2 2- - 3.8118 Å2 -0 Å2 3- - - -3.6158 Å2
精密化ステップ サイクル : LAST / 解像度 : 3.35→46.2 Åタンパク質 核酸 リガンド 溶媒 全体 原子数 11342 0 7 0 11349
拘束条件 Refine-ID タイプ Dev ideal 数 X-RAY DIFFRACTION f_bond_d0.007 11771 X-RAY DIFFRACTION f_angle_d1.11 16034 X-RAY DIFFRACTION f_chiral_restr0.069 1865 X-RAY DIFFRACTION f_plane_restr0.004 1972 X-RAY DIFFRACTION f_dihedral_angle_d18.157 3890
LS精密化 シェル Refine-ID : X-RAY DIFFRACTION / Total num. of bins used : 10
解像度 (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)3.35-3.4697 0.3109 117 0.2819 1053 1170 29 3.4697-3.6086 0.343 317 0.2529 3014 3331 83 3.6086-3.7728 0.2944 396 0.2391 3638 4034 100 3.7728-3.9716 0.2797 397 0.2232 3646 4043 100 3.9716-4.2202 0.2875 388 0.214 3656 4044 100 4.2202-4.5458 0.2901 408 0.225 3631 4039 100 4.5458-5.0028 0.2856 407 0.2321 3671 4078 100 5.0028-5.7256 0.3244 433 0.2545 3670 4103 100 5.7256-7.2092 0.3284 393 0.2628 3750 4143 100 7.2092-46.2 0.27 449 0.2426 3785 4234 98
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 0.5838 -0.1415 -0.2393 0.6325 -0.1084 0.1379 0.1925 -0.2666 0.0448 1.0093 -0.0111 0.6322 -0.2008 -0.057 0.2008 1.1016 0.1094 0.724 0.2771 -0.0475 0.4422 -17.7513 9.0029 77.9343 2 0.3757 0.2007 0.1332 0.2087 0.1886 0.2497 0.2726 -0.3736 0.2916 0.2795 -0.4636 0.1757 0.2405 0.0155 -0.1546 1.3269 -0.2079 0.897 0.2978 -0.178 0.5761 -17.3895 12.8293 75.3136 3 0.2179 -0.0376 -0.147 0.076 0.0826 0.134 0.241 0.108 0.0561 0.093 -0.225 0.1879 -0.1561 -0.2804 0.1183 0.3156 -0.0288 0.47 0.8136 -0.2624 1.1211 -37.3861 20.4962 81.7728 4 0.9351 -0.0874 -0.0641 1.3717 -0.6515 0.4084 -0.2325 -0.7132 0.1302 1.3505 0.0126 0.7513 -0.0754 -0.0575 -0.3801 1.0698 -0.1763 0.8587 0.385 -0.0794 0.5552 -22.3037 16.6527 73.2269 5 0.8805 -0.0487 0.2768 0.3779 0.3316 0.6283 0.0811 0.218 -0.2142 -0.531 -0.0503 0.2386 -0.2945 0.3229 -0.0227 0.803 -0.0615 0.0611 0.1822 0.1041 0.2618 -0.1814 -19.0281 36.0895 6 0.3694 -0.2838 0.1297 0.4668 -0.2083 0.3449 0.0102 -0.0536 -0.278 -0.3584 0.0884 0.4241 0.2939 -0.2419 -0.0821 0.1493 -0.3574 -0.145 0.4269 -0.1534 0.9055 -30.4974 24.2203 32.6736 7 0.5447 0.0988 0.7988 1.7005 0.1352 1.1657 0.174 -0.1806 -0.0855 -0.6757 -0.182 1.0816 -0.0131 -0.6279 0.1876 0.3003 -0.0193 -0.3409 0.3089 -0.1439 0.7983 -25.6214 28.4918 33.4725 8 0.0742 -0.1194 -0.2439 0.1794 0.3823 0.7866 0.094 0.2353 -0.1689 0.0909 -0.1665 0.0915 0.469 -0.3014 0.0692 0.5602 -0.1068 -0.569 0.8314 0.1778 0.6892 -24.3211 31.9511 12.5273 9 0.3604 -0.3143 0.3212 0.8962 0.2567 0.6495 -0.0954 0.159 -0.1916 -0.5279 -0.2182 0.797 -0.1121 -0.2407 0.1529 0.4326 0.0601 -0.2928 0.3214 -0.2755 0.5364 -20.6418 31.0734 30.9425 10 0.136 0.0717 0.0272 0.1226 0.0199 0.0056 -0.008 -0.0332 -0.0679 -0.0307 0.1738 0.0163 0.0108 0.0196 -0.0724 1.1359 -0.6506 -0.2094 1.6693 0.2693 0.8 -31.9943 -6.5264 43.379 11 0.0341 -0.0508 0.2191 6.6397 -2.6841 2.7067 0.182 -0.0514 0.2143 -0.4046 -0.9662 -1.7455 0.0428 0.9214 0.2833 -0.0045 -0.0027 -0.0355 0.3055 -0.0203 0.4808 24.3617 22.7906 36.3407 12 0.5687 0.2436 0.5142 2.624 -0.1465 1.2246 0.0909 0.1651 -0.1112 0.4822 -0.3144 -0.8849 0.0242 0.4122 0.2537 0.1871 -0.0313 -0.0704 0.1445 0.1181 0.2477 8.9647 10.906 50.2034 13 0.1071 -0.2179 0.2378 2.4655 -1.1344 1.392 -0.2793 0.0319 0.3 0.8144 -0.5217 -1.3774 -0.2109 0.588 0.0661 0.209 -0.1729 -0.3426 0.3963 0.145 0.756 19.2143 18.2274 53.1869 14 0.1616 -0.0036 -0.1779 3.264 -0.2797 0.4139 0.2807 -0.0694 0.0743 0.7985 -0.3417 -1.6768 0.0144 0.4428 0.2366 -0.0684 0.0764 -0.3069 0.1814 0.2124 0.8035 19.247 14.6999 51.9716 15 0.0459 0.0194 0.1547 1.4147 -0.552 0.7863 -0.1781 -0.0699 0.0861 0.0121 -0.2487 0.0349 -0.2784 -0.2204 0.3744 0.2463 0.3766 -0.3789 0.8019 -0.4385 0.7885 -15.3734 -9.7256 34.1159
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 57:154)A57 - 154 2 X-RAY DIFFRACTION 2 (chain A and resid 155:259)A155 - 259 3 X-RAY DIFFRACTION 3 (chain A and resid 260:325)A260 - 325 4 X-RAY DIFFRACTION 4 (chain A and resid 326:553)A326 - 553 5 X-RAY DIFFRACTION 5 (chain A and resid 554:589)A554 - 589 6 X-RAY DIFFRACTION 6 (chain B and resid 57:151)B57 - 151 7 X-RAY DIFFRACTION 7 (chain B and resid 152:271)B152 - 271 8 X-RAY DIFFRACTION 8 (chain B and resid 272:311)B272 - 311 9 X-RAY DIFFRACTION 9 (chain B and resid 312:546)B312 - 546 10 X-RAY DIFFRACTION 10 (chain B and resid 547:558)B547 - 558 11 X-RAY DIFFRACTION 11 (chain C and resid 57:109)C57 - 109 12 X-RAY DIFFRACTION 12 (chain C and resid 110:223)C110 - 223 13 X-RAY DIFFRACTION 13 (chain C and resid 224:373)C224 - 373 14 X-RAY DIFFRACTION 14 (chain C and resid 374:548)C374 - 548 15 X-RAY DIFFRACTION 15 (chain C and resid