ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.9_1692精密化 | Aimless | 0.5.8データスケーリング | PDB_EXTRACT | 3.2 | データ抽出 | XDS | | データ削減 | PHASER | | 位相決定 | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4YX8 解像度: 2.562→42.817 Å / SU ML: 0.32 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.67 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2216 | 3011 | 4.85 % |
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Rwork | 0.1709 | 59058 | - |
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obs | 0.1734 | 62069 | 99.32 % |
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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 |
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原子変位パラメータ | Biso max: 151.2 Å2 / Biso mean: 55.4858 Å2 / Biso min: 14.47 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.562→42.817 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 10190 | 0 | 0 | 82 | 10272 |
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Biso mean | - | - | - | 42.96 | - |
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残基数 | - | - | - | - | 1315 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.008 | 10414 | X-RAY DIFFRACTION | f_angle_d1.047 | 14102 | X-RAY DIFFRACTION | f_chiral_restr0.038 | 1675 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1831 | X-RAY DIFFRACTION | f_dihedral_angle_d13.281 | 4002 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.562-2.6018 | 0.3107 | 117 | 0.2742 | 2666 | 2783 | 100 | 2.6018-2.6445 | 0.3073 | 123 | 0.2747 | 2712 | 2835 | 100 | 2.6445-2.6901 | 0.3904 | 148 | 0.2698 | 2592 | 2740 | 98 | 2.6901-2.739 | 0.3262 | 134 | 0.268 | 2681 | 2815 | 100 | 2.739-2.7917 | 0.3096 | 136 | 0.2375 | 2731 | 2867 | 100 | 2.7917-2.8486 | 0.3136 | 153 | 0.2422 | 2638 | 2791 | 100 | 2.8486-2.9106 | 0.2687 | 113 | 0.2297 | 2714 | 2827 | 100 | 2.9106-2.9783 | 0.2685 | 152 | 0.223 | 2711 | 2863 | 100 | 2.9783-3.0527 | 0.3182 | 139 | 0.2173 | 2654 | 2793 | 100 | 3.0527-3.1352 | 0.3103 | 116 | 0.202 | 2719 | 2835 | 100 | 3.1352-3.2275 | 0.2211 | 144 | 0.2055 | 2706 | 2850 | 100 | 3.2275-3.3316 | 0.2503 | 146 | 0.1832 | 2693 | 2839 | 100 | 3.3316-3.4506 | 0.2588 | 132 | 0.1864 | 2586 | 2718 | 97 | 3.4506-3.5887 | 0.2044 | 128 | 0.1711 | 2705 | 2833 | 100 | 3.5887-3.752 | 0.2085 | 130 | 0.1536 | 2653 | 2783 | 98 | 3.752-3.9496 | 0.1959 | 135 | 0.1453 | 2599 | 2734 | 97 | 3.9496-4.1969 | 0.1791 | 157 | 0.1292 | 2705 | 2862 | 100 | 4.1969-4.5206 | 0.1649 | 133 | 0.1168 | 2669 | 2802 | 100 | 4.5206-4.9749 | 0.1864 | 136 | 0.1272 | 2730 | 2866 | 100 | 4.9749-5.6934 | 0.201 | 132 | 0.1464 | 2727 | 2859 | 100 | 5.6934-7.1676 | 0.1955 | 133 | 0.1614 | 2753 | 2886 | 100 | 7.1676-42.8232 | 0.1647 | 174 | 0.1411 | 2714 | 2888 | 99 |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION 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) |
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1 | 0.2334 | 0.0072 | -0.0016 | 0.2589 | -0.1489 | -0.0582 | 0.0475 | 0.0346 | -0.0129 | -0.0052 | -0.0756 | -0.1702 | -0.0342 | 0.0917 | -0 | 0.3313 | 0.0403 | 0.0799 | 0.2891 | 0.0005 | 0.3592 | 54.8431 | -16.452 | 82.2719 | 2 | 0.285 | 0.2565 | 0.2926 | 0.486 | 0.1012 | 0.5142 | -0.0567 | -0.0322 | -0.1548 | -0.0262 | 0.0322 | -0.0309 | 0.0155 | 0.008 | -0 | 0.2375 | 0.0526 | 0.0056 | 0.1917 | -0.0026 | 0.2807 | 38.3035 | -38.4367 | 93.8724 | 3 | 0.3782 | -0.1952 | -0.0407 | 0.8105 | 0.6642 | 0.8553 | 0.0655 | -0.0466 | -0.0173 | -0.0249 | -0.002 | -0.0915 | -0.2292 | -0.0529 | -0 | 0.3136 | 0.0405 | 0.0113 | 0.2352 | 0.0224 | 0.3164 | 41.467 | -33.9816 | 95.4019 | 4 | 0.1342 | 0.0741 | 0.2185 | 0.1559 | 0.1704 | 0.3475 | 0.3492 | 0.4084 | 0.1804 | 0.0242 | -0.2866 | -0.0502 | -0.0763 | 0.1459 | -0.0002 | 0.521 | 0.036 | 0.0572 | 0.6139 | 0.0376 | 0.4806 | 63.053 | 4.0068 | 70.8353 | 5 | 0.2497 | 0.2892 | 0.153 | 0.2498 | 0.0606 | 0.1641 | -0.0306 | -0.0587 | -0.2246 | 0.0945 | -0.051 | 0.1981 | 0.1805 | -0.1193 | -0.0001 | 0.3513 | -0.0372 | 0.0234 | 0.1406 | -0.0119 | 0.353 | 39.444 | -11.5444 | 81.7553 | 6 | 0.8039 | -0.2156 | -0.5688 | 1.1933 | 0.1877 | 1.1945 | 0.0011 | 0.1084 | 0.0306 | -0.0963 | -0.0473 | 0.0174 | 0.0458 | -0.2278 | -0 | 0.2944 | -0.0602 | 0.0009 | 0.2661 | 0.0111 | 0.2865 | 30.3628 | -0.0502 | 81.1688 | 7 | 0.2457 | 0.229 | 0.0887 | 0.2409 | 0.1436 | 0.0694 | -0.114 | 0.0905 | -0.2368 | -0.1887 | 0.0698 | 0.1611 | 0.0467 | 0.2385 | -0.0001 | 0.5003 | 0.042 | 0.1059 | 0.4624 | -0.0278 | 0.4668 | 61.4318 | 2.0268 | 72.4673 | 8 | 0.3905 | -0.2392 | -0.1774 | 0.7645 | -0.364 | 1.0371 | 0.0927 | 0.1711 | -0.0185 | -0.2073 | -0.0458 | -0.178 | -0.0127 | -0.2748 | 0 | 0.311 | -0.0727 | 0.0363 | 0.3256 | 0.0301 | 0.2706 | 36.939 | 20.4827 | 61.7548 | 9 | 0.202 | -0.1126 | 0.0703 | 0.4338 | -0.2282 | 1.9132 | 0.1354 | 0.0511 | -0.0697 | -0.1354 | -0.0579 | -0.0207 | 0.2528 | -0.2694 | 0.0291 | 0.2007 | -0.0067 | 0.0468 | 0.1794 | 0.004 | 0.1152 | 37.7437 | 16.4436 | 58.7561 | 10 | 0.1861 | 0.06 | 0.1081 | 0.1485 | -0.0365 | 0.0517 | -0.044 | 0.2961 | -0.2096 | 0.1421 | 0.1607 | -0.2325 | 0.2568 | -0.3923 | -0.0002 | 0.2455 | 0.0008 | -0.0341 | 0.2213 | 0.023 | 0.329 | 52.6203 | -45.8239 | 128.5133 | 11 | 0.2509 | 0.0242 | 0.1422 | 0.2223 | -0.1289 | 0.2417 | -0.0626 | 0.1276 | 0.0633 | -0.0873 | 0.0734 | -0.0458 | 0.1617 | -0.0148 | 0 | 0.354 | 0.0597 | -0.0229 | 0.2797 | 0.0325 | 0.3543 | 54.0075 | -17.3257 | 111.3417 | 12 | 0.7166 | 0.2028 | -0.1946 | 1.2056 | -0.0403 | 1.2583 | 0.0454 | 0.0056 | 0.0076 | 0.1282 | -0.0328 | -0.2035 | -0.0161 | 0.0898 | 0 | 0.2708 | -0.0032 | -0.0192 | 0.2165 | 0.0384 | 0.3257 | 54.0863 | 7.2992 | 100.6441 | 13 | 0.2154 | 0.2583 | 0.0189 | 0.5061 | -0.2066 | 0.4371 | 0.1532 | -0.4196 | -0.1264 | -0.3787 | 0.0675 | -0.0594 | -0.0423 | -0.324 | -0.0001 | 0.3027 | 0.0158 | -0.0253 | 0.3404 | 0.0019 | 0.3211 | 49.639 | -38.1025 | 124.417 | 14 | 0.7421 | -0.0472 | 0.2086 | 0.5846 | 0.3287 | 1.9799 | -0.2176 | -0.0103 | 0.635 | 0.147 | -0.0605 | -0.0734 | -0.2934 | -0.5529 | -0.0528 | 0.5114 | -0.044 | -0.0569 | -0.0146 | -0.0395 | 0.3246 | 38.5261 | -12.141 | 112.9822 | 15 | 0.9078 | 0.1628 | 0.4708 | 0.8776 | -0.5326 | 1.2432 | -0.0707 | -0.2158 | 0.0356 | 0.1093 | -0.0504 | 0.0454 | -0.2428 | -0.2707 | -0.0004 | 0.3831 | 0.1079 | -0.0083 | 0.2557 | -0.0556 | 0.2625 | 24.9918 | -16.5225 | 113.5243 | 16 | 0.3749 | -0.0464 | -0.3086 | 0.4579 | -0.0118 | 0.4259 | 0.1314 | -0.0445 | 0.1013 | 0.108 | -0.0901 | 0.0149 | 0.0946 | -0.0096 | 0 | 0.3018 | 0.0022 | -0.014 | 0.1928 | -0.0098 | 0.2806 | 42.3476 | -38.8117 | 123.2457 | 17 | 0.21 | 0.4579 | -0.3047 | 0.1473 | -0.2191 | 1.7034 | 0.0796 | -0.2792 | 0.0333 | -0.0447 | -0.0364 | -0.0159 | -0.3168 | -0.2563 | 0.0007 | 0.2793 | 0.0877 | -0.0031 | 0.4476 | 0.0012 | 0.2644 | 20.1747 | -35.0576 | 135.7199 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 4 through 85 )A4 - 85 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 86 through 147 )A86 - 147 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 148 through 222 )A148 - 222 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 4 through 37 )B4 - 37 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 38 through 64 )B38 - 64 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 65 through 222 )B65 - 222 | 7 | X-RAY DIFFRACTION | 7 | chain 'C' and (resid 5 through 42 )C5 - 42 | 8 | X-RAY DIFFRACTION | 8 | chain 'C' and (resid 43 through 123 )C43 - 123 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 124 through 222 )C124 - 222 | 10 | X-RAY DIFFRACTION | 10 | chain 'D' and (resid 2 through 20 )D2 - 20 | 11 | X-RAY DIFFRACTION | 11 | chain 'D' and (resid 21 through 62 )D21 - 62 | 12 | X-RAY DIFFRACTION | 12 | chain 'D' and (resid 63 through 222 )D63 - 222 | 13 | X-RAY DIFFRACTION | 13 | chain 'E' and (resid 3 through 37 )E | | | | | | | | | | | | | | | | | | | | | | | | | |
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