ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (PHENIX.REFINE)精密化 | XDS | | データ削減 | XDS | | データスケーリング | 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: FAB FRAGMENT FROM PDB ENTRY 3T3P 解像度: 2→38.147 Å / SU ML: 0.19 / σ(F): 2.71 / 位相誤差: 21.09 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2185 | 994 | 2.5 % |
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Rwork | 0.1877 | - | - |
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obs | 0.1884 | 40075 | 96.74 % |
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溶媒の処理 | 減衰半径: 0.5 Å / VDWプローブ半径: 0.9 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso mean: 34.8 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2→38.147 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3297 | 0 | 0 | 350 | 3647 |
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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_d0.007 | 3390 | X-RAY DIFFRACTION | f_angle_d1.149 | 4617 | X-RAY DIFFRACTION | f_dihedral_angle_d12.927 | 1207 | X-RAY DIFFRACTION | f_chiral_restr0.066 | 524 | X-RAY DIFFRACTION | f_plane_restr0.006 | 585 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2-2.1055 | 0.2312 | 116 | 0.2026 | 4698 | X-RAY DIFFRACTION | 83 | 2.1055-2.2374 | 0.2297 | 146 | 0.2048 | 5612 | X-RAY DIFFRACTION | 98 | 2.2374-2.4101 | 0.2331 | 146 | 0.2075 | 5662 | X-RAY DIFFRACTION | 100 | 2.4101-2.6526 | 0.2431 | 150 | 0.2071 | 5720 | X-RAY DIFFRACTION | 100 | 2.6526-3.0363 | 0.2461 | 143 | 0.1906 | 5742 | X-RAY DIFFRACTION | 100 | 3.0363-3.8249 | 0.216 | 147 | 0.169 | 5761 | X-RAY DIFFRACTION | 99 | 3.8249-38.154 | 0.1875 | 146 | 0.1793 | 5886 | X-RAY DIFFRACTION | 97 |
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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 | 0.9925 | 0.2991 | 0.2864 | 0.9232 | -0.7649 | 0.849 | 0.2558 | -0.0729 | 0.14 | 0.8154 | -0.247 | -0.2468 | 0.3522 | -0.7419 | -0.0008 | 0.3446 | -0.0282 | 0.0196 | 0.3396 | 0.0357 | 0.3169 | 19.4412 | -19.4665 | 13.0846 | 2 | 0.23 | 0.3888 | 0.3574 | 1.0171 | -0.1603 | 0.5193 | -0.0493 | -0.1194 | -0.0349 | 0.0947 | 0.1675 | 0.1714 | 0.1886 | -0.1362 | 0 | 0.2605 | 0.001 | -0.0096 | 0.2932 | 0.008 | 0.3934 | 19.105 | -19.1098 | 4.6631 | 3 | 1.3814 | 0.887 | 0.7154 | 1.0238 | -0.054 | 1.617 | -0.0982 | -0.054 | 0.0964 | 0.2855 | 0.0644 | -0.0301 | 0.2153 | -0.0988 | -0.0004 | 0.2627 | 0.0059 | -0.0309 | 0.2162 | 0.0101 | 0.2897 | 26.2488 | -11.8394 | 6.7792 | 4 | 0.0467 | -0.02 | 0.0387 | 0.4184 | 0.0058 | 0.099 | -0.9319 | -0.4971 | -0.922 | -0.5945 | -0.1075 | -1.4773 | 1.4666 | 1.2104 | 0.0044 | 0.6627 | 0.1229 | -0.0923 | 0.5563 | 0.0491 | 1.1587 | 39.8842 | -21.6338 | 8.9447 | 5 | 1.0204 | 0.7884 | -1.1261 | 1.7092 | 0.8853 | 2.2687 | 0.0401 | 0.4447 | 0.0705 | -0.3301 | -0.1357 | 0.09 | -0.1498 | -0.0096 | 0.0003 | 0.2665 | -0.0195 | -0.025 | 0.2366 | 0.0184 | 0.2563 | 25.3332 | -8.1976 | 0.481 | 6 | 0.2542 | -0.3589 | -0.2845 | 0.5127 | 0.0402 | 1.0716 | -0.2707 | 0.5305 | 0.4047 | -0.2171 | 0.1934 | -0.395 | -0.4166 | -0.0183 | -0.0009 | 0.3572 | -0.0188 | -0.0075 | 0.2699 | -0.0153 | 0.3229 | 29.2166 | -15.1133 | -5.2096 | 7 | 0.6419 | 0.2729 | 0.6782 | 1.0878 | -0.6234 | 1.6164 | 0.0652 | -0.0011 | 0.0475 | -0.0862 | -0.0593 | 0.1966 | -0.1455 | -0.1102 | -0.0001 | 0.2605 | 0.0152 | -0.0128 | 0.2587 | 0.0139 | 0.3278 | 16.5603 | -15.4926 | 1.9192 | 8 | 0.2223 | 0.192 | -0.0095 | 0.1736 | 0.1152 | 0.3829 | -0.1043 | 0.6373 | -0.7581 | -0.4086 | 0.2873 | -0.8858 | -0.1831 | 1.0302 | -0.0008 | 0.3249 | 0.0229 | -0.0177 | 0.4049 | -0.0651 | 0.3572 | 32.5595 | -26.451 | -2.8625 | 9 | 1.2651 | -0.6454 | 1.3343 | 0.5592 | -0.6424 | 0.8637 | -0.0126 | -0.1003 | 0.1057 | 0.1713 | 0.0463 | 0.1155 | -0.0346 | -0.0199 | 0.0004 | 0.2692 | -0.0052 | 0.0228 | 0.2389 | -0.0114 | 0.2637 | 26.2543 | -12.0738 | 10.2611 | 10 | 0.2847 | -0.034 | -0.4482 | 0.396 | -0.2741 | 0.4272 | -0.0333 | -0.1281 | 0.2935 | 0.0926 | 0.0447 | -0.137 | 0.0379 | 0.0953 | 0.0003 | 0.2494 | -0.0088 | -0.0052 | 0.308 | -0.0221 | 0.3417 | 25.7415 | -0.1143 | 9.108 | 11 | 0.6983 | 0.1759 | 0.7408 | 0.3865 | -0.1472 | 0.8616 | 0.0625 | 0.0237 | 0.0131 | 0.4301 | 0.0683 | -0.1527 | 0.3314 | -0.0098 | 0.0001 | 0.2496 | 0.0174 | 0.0068 | 0.2236 | 0.0075 | 0.2747 | 26.6711 | -22.3223 | 8.9498 | 12 | 1.7803 | -0.343 | -1.0851 | 3.6125 | 0.883 | 1.2875 | 0.1687 | -0.2897 | -0.557 | 0.3487 | 0.0148 | 0.0797 | 0.3926 | 0.1931 | 0.0025 | 0.2917 | 0.0113 | 0.038 | 0.2919 | 0.076 | 0.3892 | 39.2046 | -48.5168 | 18.9224 | 13 | 0.41 | -0.0156 | 0.2085 | 0.1874 | 0.1521 | 0.1716 | 0.8549 | 0.3118 | -0.4767 | -0.143 | -0.3462 | 0.4088 | 0.9271 | 0.0967 | -0.0002 | 0.344 | 0.0203 | -0.0297 | 0.2984 | 0.0032 | 0.3558 | 37.7182 | -46.4775 | 14.4811 | 14 | 1.2615 | -0.2931 | -0.4602 | 0.9583 | 0.7198 | 0.5322 | 0.0089 | -0.343 | -0.2046 | 0.1036 | -0.2024 | 0.3624 | 0.081 | 0.0247 | 0.0001 | 0.3108 | 0.0123 | 0.0274 | 0.354 | 0.0236 | 0.4072 | 30.9793 | -42.0467 | 18.7781 | 15 | 2.9598 | 1.4265 | 0.888 | 2.5116 | -0.1641 | 0.3399 | -0.137 | -0.3094 | -0.0086 | 0.0715 | 0.1346 | 0.2441 | 0.1845 | -0.5128 | 0.0018 | 0.3604 | 0.0501 | 0.0208 | 0.3192 | -0.0046 | 0.3561 | 38.8515 | -38.8411 | 20.2752 | 16 | 1.3672 | -0.1342 | 0.4036 | 0.4895 | 0.0925 | 0.2062 | 0.0065 | 0.994 | -0.4207 | -0.343 | 0.0729 | -0.0467 | -0.3035 | 1.1739 | -0.0176 | 0.3474 | 0.0316 | -0.0248 | 0.3285 | -0.0377 | 0.3606 | 36.1119 | -40.4167 | 6.7191 | 17 | 0.5954 | 0.0198 | -0.2881 | 0.887 | 0.5548 | 0.3766 | -0.1174 | -0.7625 | -0.5875 | 0.695 | 0.0968 | 0.5425 | 0.5826 | 0.1793 | -0.0094 | 0.5395 | 0.0527 | 0.0806 | 0.5335 | 0.1754 | 0.3703 | 42.2143 | -48.2048 | 30.297 | 18 | 0.4885 | 0.0254 | -0.1151 | 0.3192 | 0.2392 | 0.1615 | -0.0683 | -0.1894 | -0.3645 | 1.1391 | -0.0986 | 0.2352 | 0.1385 | 0.0881 | -0.002 | 0.6384 | -0.0064 | 0.0432 | 0.5298 | 0.1296 | 0.4793 | 35.1244 | -52.1897 | 28.2417 | 19 | 0.0693 | -0.0293 | -0.0903 | 0.0343 | -0.0093 | 0.1223 | -0.1103 | -0.3807 | -0.696 | 0.3373 | 0.4891 | 0.6341 | 0.4977 | -0.7376 | 0.0013 | 0.3272 | -0.0428 | -0.0017 | 0.3621 | -0.0154 | 0.4691 | 23.9673 | -43.236 | 13.0053 | 20 | 0.2836 | 0.0914 | 0.6657 | 0.3093 | 0.2415 | 0.9919 | -0.0622 | -0.3989 | -0.9815 | 0.1548 | 0.2611 | 0.3959 | 0.3075 | -0.2523 | 0.0065 | 0.5277 | -0.0994 | 0.0499 | 0.4009 | 0.1722 | 0.656 | 34.6233 | -53.8487 | 21.5019 | 21 | 0.7538 | 0.7259 | -0.3679 | 1.0541 | -0.2395 | 0.4365 | -0.1232 | 0.0685 | -0.0872 | -0.0799 | -0.0939 | -0.7156 | 0.5653 | 0.433 | 0.0007 | 0.398 | 0.054 | -0.0288 | 0.3675 | -0.0087 | 0.3039 | 45.6677 | -10.1153 | 10.9998 | 22 | 0.1052 | -0.0794 | -0.1197 | 0.0818 | 0.066 | 0.0601 | 0.0354 | -0.2451 | 0.1559 | 0.111 | -0.2173 | -1.0853 | -0.3572 | 0.4829 | 0.0066 | 0.4722 | 0.0705 | -0.0333 | 0.3519 | -0.0422 | 0.4002 | 46.3173 | -15.7423 | 31.042 | 23 | 0.6959 | 0.2673 | -0.1626 | 0.4004 | -0.0313 | 0.1983 | -0.2425 | 0.1284 | 0.3069 | 0.3997 | -0.0314 | 0.0065 | -1.2119 | -0.8983 | 0.0002 | 0.441 | 0.001 | -0.0655 | 0.3407 | -0.0153 | 0.4248 | 45.5458 | -7.6031 | 23.9517 | 24 | 0.528 | 0.6243 | -0.3214 | 1.0456 | 0.222 | 1.1584 | 0.0178 | -0.1057 | 0.2219 | 0.1167 | 0.1599 | -0.2632 | -0.3569 | 0.4759 | 0 | 0.3251 | -0.022 | -0.0412 | 0.2983 | 0.0063 | 0.2606 | 42.1595 | 0.9124 | 10.156 | 25 | 0.6354 | -0.1276 | 0.4086 | 0.4111 | 0.2047 | 0.4244 | 0.1887 | -0.2811 | 0.1708 | 0.2 | -0.2112 | 0.3079 | 0.4649 | 0.1026 | 0.0017 | 0.3493 | 0.0447 | 0.0303 | 0.2442 | 0.0213 | 0.2463 | 34.9473 | -11.9311 | 18.7167 | 26 | 0.4253 | -0.1189 | -0.4739 | 0.4374 | 0.9132 | 2.082 | 0.0704 | -0.0629 | -0.0674 | 0.3137 | -0.1095 | 0.5988 | 0.2619 | -0.152 | -0.0003 | 0.34 | 0.0174 | 0.0012 | 0.269 | 0.0062 | 0.2814 | 31.543 | -10.319 | 19.4377 | 27 | 0.9536 | -0.2943 | -0.4347 | 0.7805 | 0.8085 | 1.1211 | -0.0552 | -0.0381 | -0.1362 | 0.2869 | 0.1723 | 0.277 | -0.0728 | -0.4068 | -0.0008 | 0.4167 | -0.0037 | 0.0059 | 0.3053 | 0.0078 | 0.2775 | 32.3521 | -4.172 | 25.9511 | 28 | 0.7891 | 0.1399 | 0.5393 | 0.3226 | 0.5351 | 0.7351 | -0.0188 | -0.161 | 0.0247 | 0.3971 | -0.0398 | -0.0188 | -0.4549 | 0.3971 | 0.0001 | 0.3134 | 0.0166 | -0.0211 | 0.2597 | -0.0031 | 0.2573 | 43.2924 | -2.0988 | 20.8262 | 29 | 0.1094 | -0.037 | -0.0897 | 0.3723 | 0.0399 | 0.2893 | 0.2794 | -0.4774 | 0.0186 | 1.7654 | -0.0588 | 0.9754 | 0.6157 | -0.4179 | 0.0017 | 0.6334 | -0.0108 | 0.0499 | 0.3882 | -0.0397 | 0.501 | 37.9338 | -15.3081 | 32.8411 | 30 | 1.1126 | 0.0733 | 0.211 | 1.0139 | 0.6692 | 1.1254 | 0.0024 | 0.0398 | 0.0033 | 0.1517 | 0.0357 | 0.0725 | -0.0076 | 0.2656 | -0 | 0.2698 | -0.0107 | -0.0152 | 0.2116 | -0.0059 | 0.2378 | 37.7542 | -9.2375 | 12.5424 | 31 | -0.0064 | -0.4068 | -0.0606 | 0.3324 | -0.2692 | 0.4099 | -0.0153 | -0.2622 | 0.1262 | 0.3127 | 0.3181 | 0.0735 | 0.0531 | -0.2656 | 0.0002 | 0.4099 | 0.0308 | -0.067 | 0.3524 | -0.0208 | 0.2832 | 46.2865 | -20.5881 | 26.6037 | 32 | 1.0664 | -1.7345 | 0.3836 | 1.7908 | -0.086 | 1.4786 | -0.003 | -0.1168 | -0.3213 | 0.5815 | 0.1707 | -0.1056 | 0.3195 | -0.0264 | 0.0036 | 0.3448 | 0.051 | 0.01 | 0.2905 | 0.0113 | 0.2328 | 48.4898 | -45.5446 | 20.9384 | 33 | 1.7255 | -1.2588 | -0.0245 | 1.4713 | -0.2673 | 0.0349 | 0.0801 | -0.0592 | -0.3235 | 0.1774 | -0.0328 | 0.025 | 0.0541 | -0.1791 | -0.0002 | 0.3135 | 0.0367 | -0.0111 | 0.3058 | 0.0057 | 0.2745 | 47.2166 | -42.944 | 17.9048 | 34 | 0.13 | 0.1582 | 0.1795 | 0.5017 | 0.7349 | 1.0666 | 0.1425 | -0.0291 | 0.3325 | -0.5127 | 0.391 | -0.8967 | -0.5692 | 0.251 | 0.0041 | 0.4164 | 0.0072 | 0.0201 | 0.3151 | 0.0003 | 0.3768 | 55.3267 | -36.1674 | 15.578 | 35 | 0.5821 | 0.1405 | -0.367 | 0.2156 | 0.1283 | 0.4688 | -0.3711 | 0.2011 | 0.3916 | -0.3211 | 0.3632 | -0.3246 | -0.3971 | 0.1954 | 0.0006 | 0.4637 | 0.0489 | -0.0022 | 0.3794 | 0.0094 | 0.3954 | 58.8754 | -45.4345 | 7.5541 | 36 | 1.5908 | -0.8717 | 1.9871 | 3.2231 | 0.2689 | 1.5858 | -0.1671 | -0.0762 | -0.0329 | 0.052 | -0.057 | 0.3206 | -0.1755 | -0.019 | -0.0003 | 0.2979 | 0.0172 | -0.0182 | 0.2433 | 0.0165 | 0.2428 | 45.6139 | -34.5949 | 19.1865 | 37 | 0.5801 | -0.667 | -0.0335 | 0.5154 | 0.0607 | 0.429 | -0.257 | 0.2119 | -0.2482 | -0.7983 | -0.2698 | 0.4284 | 0.042 | -0.2538 | 0.0005 | 0.4648 | 0.0703 | -0.0428 | 0.341 | -0.01 | 0.4073 | 50.6853 | -55.2822 | 4.8799 | 38 | -0.0485 | 0.1535 | 0.2602 | 0.3942 | -0.0523 | 0.474 | -0.1818 | -0.0495 | 0.0664 | -0.4295 | 0.4049 | -0.2535 | -0.2079 | 0.6614 | -0.0001 | 0.3394 | 0.0523 | -0.0211 | 0.3013 | -0.0135 | 0.3558 | 57.5219 | -47.2056 | 14.2352 | 39 | 0.463 | 0.1461 | 0.109 | 0.2406 | -0.1992 | 0.4058 | -0.4664 | -0.8143 | 1.0426 | 0.0162 | 0.8945 | -1.5195 | -0.4698 | 0.3151 | 0.0018 | 0.4434 | 0.003 | -0.1052 | 0.4122 | -0.1309 | 0.5076 | 61.7558 | -33.3615 | 24.0603 | 40 | 0.455 | -0.1113 | 0.6296 | 0.1288 | -0.2155 | 0.5661 | -0.1534 | 0.0183 | -0.2342 | 0.8067 | 0.3922 | -0.4649 | 0.5347 | 0.2643 | 0.0013 | 0.407 | 0.0407 | -0.0155 | 0.3853 | 0.0077 | 0.4641 | 56.6038 | -51.6063 | 18.4351 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | (CHAIN H AND RESID 1:10)2 | X-RAY DIFFRACTION | 2 | (CHAIN H AND RESID 11:30)3 | X-RAY DIFFRACTION | 3 | (CHAIN H AND RESID 31:40)4 | X-RAY DIFFRACTION | 4 | (CHAIN H AND RESID 41:44)5 | X-RAY DIFFRACTION | 5 | (CHAIN H AND RESID 45:62)6 | X-RAY DIFFRACTION | 6 | (CHAIN H AND RESID 63:69)7 | X-RAY DIFFRACTION | 7 | (CHAIN H AND RESID 70:84)8 | X-RAY DIFFRACTION | 8 | (CHAIN H AND RESID 85:91)9 | X-RAY DIFFRACTION | 9 | (CHAIN H AND RESID 92:101)10 | X-RAY DIFFRACTION | 10 | (CHAIN H AND RESID 102:109)11 | X-RAY DIFFRACTION | 11 | (CHAIN H AND RESID 110:123)12 | X-RAY DIFFRACTION | 12 | (CHAIN H AND RESID 124:148)13 | X-RAY DIFFRACTION | 13 | (CHAIN H AND RESID 149:152)14 | X-RAY DIFFRACTION | 14 | (CHAIN H AND RESID 153:167)15 | X-RAY DIFFRACTION | 15 | (CHAIN H AND RESID 168:180)16 | X-RAY DIFFRACTION | 16 | (CHAIN H AND RESID 181:186)17 | X-RAY DIFFRACTION | 17 | (CHAIN H AND RESID 187:197)18 | X-RAY DIFFRACTION | 18 | (CHAIN H AND | | | | | | | | | | | | | | | | | |
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