ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データスケーリング | PHENIX | 1.8.2_1309精密化 | PDB_EXTRACT | 3.15 | データ抽出 | HKL-2000 | | 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: 5DRN 解像度: 1.95→41.2 Å / FOM work R set: 0.8319 / SU ML: 0.21 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.65 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2235 | 3971 | 5.06 % |
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Rwork | 0.1827 | 74432 | - |
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obs | 0.1847 | 78403 | 99.64 % |
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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: 131.15 Å2 / Biso mean: 49.44 Å2 / Biso min: 19.92 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.95→41.2 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6239 | 0 | 74 | 242 | 6555 |
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Biso mean | - | - | 60.94 | 45.63 | - |
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残基数 | - | - | - | - | 837 |
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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_d0.014 | 6486 | X-RAY DIFFRACTION | f_angle_d1.496 | 8868 | X-RAY DIFFRACTION | f_chiral_restr0.122 | 1052 | X-RAY DIFFRACTION | f_plane_restr0.007 | 1111 | X-RAY DIFFRACTION | f_dihedral_angle_d12.734 | 2248 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.9503-1.9741 | 0.3091 | 126 | 0.2703 | 2497 | 2623 | 94 | 1.9741-1.9991 | 0.2781 | 149 | 0.2406 | 2576 | 2725 | 99 | 1.9991-2.0254 | 0.2461 | 148 | 0.223 | 2651 | 2799 | 100 | 2.0254-2.0532 | 0.2463 | 150 | 0.2227 | 2590 | 2740 | 100 | 2.0532-2.0825 | 0.2439 | 122 | 0.2153 | 2714 | 2836 | 100 | 2.0825-2.1136 | 0.2468 | 133 | 0.2043 | 2577 | 2710 | 100 | 2.1136-2.1466 | 0.2512 | 148 | 0.2072 | 2667 | 2815 | 100 | 2.1466-2.1818 | 0.2775 | 159 | 0.2023 | 2596 | 2755 | 100 | 2.1818-2.2194 | 0.2323 | 127 | 0.2102 | 2677 | 2804 | 100 | 2.2194-2.2598 | 0.2779 | 136 | 0.1916 | 2634 | 2770 | 100 | 2.2598-2.3032 | 0.2408 | 147 | 0.2003 | 2658 | 2805 | 100 | 2.3032-2.3502 | 0.2305 | 142 | 0.196 | 2618 | 2760 | 100 | 2.3502-2.4013 | 0.2773 | 123 | 0.1926 | 2670 | 2793 | 100 | 2.4013-2.4572 | 0.2387 | 153 | 0.1923 | 2632 | 2785 | 100 | 2.4572-2.5186 | 0.2572 | 151 | 0.1925 | 2658 | 2809 | 100 | 2.5186-2.5867 | 0.2544 | 122 | 0.1926 | 2675 | 2797 | 100 | 2.5867-2.6628 | 0.2715 | 148 | 0.1894 | 2645 | 2793 | 100 | 2.6628-2.7487 | 0.2553 | 147 | 0.1962 | 2667 | 2814 | 100 | 2.7487-2.847 | 0.2902 | 139 | 0.21 | 2669 | 2808 | 100 | 2.847-2.9609 | 0.2365 | 152 | 0.2029 | 2641 | 2793 | 100 | 2.9609-3.0956 | 0.233 | 147 | 0.202 | 2669 | 2816 | 100 | 3.0956-3.2588 | 0.2428 | 146 | 0.1994 | 2664 | 2810 | 100 | 3.2588-3.4628 | 0.2188 | 135 | 0.1928 | 2700 | 2835 | 100 | 3.4628-3.7301 | 0.218 | 127 | 0.1742 | 2701 | 2828 | 100 | 3.7301-4.1051 | 0.1931 | 131 | 0.1647 | 2716 | 2847 | 100 | 4.1051-4.6984 | 0.1551 | 140 | 0.1374 | 2721 | 2861 | 100 | 4.6984-5.9167 | 0.2016 | 161 | 0.1518 | 2729 | 2890 | 100 | 5.9167-41.1888 | 0.2279 | 162 | 0.1948 | 2820 | 2982 | 98 |
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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 | 0.1473 | 0.5539 | 0.1091 | 0.749 | -0.0932 | 0.2615 | -0.018 | -0.3698 | -0.1892 | 0.1626 | -0.059 | -0.3527 | 0.5709 | 0.3425 | 0.0002 | 0.4118 | 0.0102 | -0.0086 | 0.3744 | 0.0124 | 0.3585 | 40.231 | 122.6913 | 19.858 | 2 | 2.2926 | 0.0531 | 0.1487 | 2.8285 | 0.9318 | 1.055 | 0.0739 | 0.062 | -0.1437 | -0.0812 | -0.1066 | -0.085 | 0.1736 | -0.0045 | -0.0001 | 0.3509 | -0.0147 | -0.0367 | 0.2309 | 0.011 | 0.2874 | 29.454 | 116.1153 | 21.4376 | 3 | 1.4674 | -0.4862 | -0.3762 | 0.9551 | 0.9214 | 1.6661 | -0.0032 | 0.0028 | -0.2545 | -0.0183 | -0.0341 | 0.1534 | 0.1542 | -0.2517 | 0.0003 | 0.3628 | -0.0169 | -0.0128 | 0.2848 | 0.0058 | 0.3281 | 29.1873 | 123.4855 | 22.0709 | 4 | 1.6063 | 0.6388 | 0.8316 | 0.3195 | -0.0456 | 0.9455 | -0.2204 | -0.2375 | 0.0837 | -0.3991 | -0.0068 | -0.0223 | -0.4326 | 0.0407 | -0.0056 | 0.4103 | 0.056 | -0.0204 | 0.2573 | -0.0061 | 0.2379 | 42.4064 | 156.1615 | 19.6684 | 5 | 1.3965 | 0.0788 | -0.0996 | 1.8176 | -1.1121 | 0.5586 | -0.036 | 0.0207 | -0.1013 | -0.0716 | 0.0999 | 0.202 | 0.044 | -0.3447 | 0.0003 | 0.288 | 0.0011 | -0.0035 | 0.3234 | 0.0026 | 0.1863 | 38.7825 | 146.6565 | 20.6127 | 6 | 2.0197 | 0.3567 | 0.6376 | 0.4176 | -0.5399 | 1.1945 | -0.1342 | -0.0586 | 0.1785 | 0.5897 | -0.0213 | -0.289 | -0.1508 | -0.0918 | 0.0003 | 0.3726 | 0.0318 | -0.0093 | 0.2681 | -0.0107 | 0.1924 | 46.8093 | 151.5797 | 25.7959 | 7 | -0.1981 | -0.585 | 0.8088 | 1.851 | 0.3957 | 0.1858 | 0.1195 | -0.0664 | -0.0478 | -0.7796 | -0.174 | 0.3974 | 0.2364 | -0.377 | -0.0509 | 0.3702 | 0.0134 | -0.1076 | 0.4395 | -0.0715 | 0.4123 | 9.4346 | 132.7157 | 18.6156 | 8 | 0.9793 | -1.0215 | 0.3758 | 0.9348 | -0.3246 | 1.0261 | 0.3465 | -0.1 | -0.0475 | 0.315 | -0.2667 | 0.3908 | 0.5059 | -0.3382 | 0.0026 | 0.3218 | -0.097 | -0.0773 | 0.3386 | -0.0378 | 0.3537 | 11.549 | 121.7178 | 23.1865 | 9 | 0.8939 | -0.7927 | 0.2941 | 0.5205 | 0.257 | 0.8383 | 0.0469 | -0.0966 | 0.1818 | 0.349 | -0.0432 | 0.038 | 0.1538 | 0.0951 | 0 | 0.2681 | -0.0664 | -0.0041 | 0.3404 | 0.0014 | 0.3548 | 15.7677 | 129.6045 | 32.0086 | 10 | 0.3048 | -0.3126 | 0.2464 | 0.8436 | -0.8874 | 1.2394 | 0.1719 | 0.0406 | 0.0141 | -0.2915 | -0.2349 | 0.4094 | 0.0162 | -0.0899 | 0.0001 | 0.2845 | -0.0312 | -0.0511 | 0.3222 | -0.0707 | 0.4223 | 10.5301 | 132.1172 | 25.8199 | 11 | 0.326 | 0.0585 | 0.0226 | 0.6996 | 0.2867 | 0.0988 | -0.1341 | 0.0092 | -0.0155 | -1.2746 | 0.1268 | 0.3167 | 0.0969 | -0.47 | 0.003 | 0.512 | -0.0275 | -0.1463 | 0.3554 | -0.0549 | 0.3953 | 17.1056 | 118.1872 | 16.3648 | 12 | -0.0042 | 0.3082 | -0.2452 | 0.2235 | -0.3211 | 0.3023 | 0.1695 | 0.0705 | 0.0523 | -0.085 | -0.0389 | 0.2001 | -0.0142 | -0.0426 | 0.0001 | 0.3254 | 0.0292 | -0.0051 | 0.3505 | 0.0075 | 0.3719 | 15.1074 | 149.4703 | 23.2663 | 13 | 0.2118 | -0.0951 | 0.1237 | 0.1262 | -0.0347 | 0.0729 | -0.0474 | 0.2015 | 0.3666 | 0.0851 | -0.0535 | 0 | 0.1137 | 0.0503 | -0.0003 | 0.3498 | 0.0211 | 0.0477 | 0.3975 | 0.0599 | 0.3061 | 41.2171 | 159.3986 | 13.0531 | 14 | 2.3114 | -0.4844 | -0.6676 | 0.339 | 0.2253 | 0.3567 | 0.038 | 0.2337 | 0.1234 | -0.1586 | -0.0566 | 0.1579 | 0.0958 | -0.0765 | 0.0001 | 0.3287 | 0.0189 | -0.0191 | 0.3545 | 0.0144 | 0.2486 | 26.6993 | 154.6195 | 14.4326 | 15 | 0.9592 | -0.7956 | -0.0906 | 0.4441 | -0.1856 | 0.4003 | -0.1973 | 1.2731 | 0.1906 | -0.2726 | 0.1909 | -0.0746 | 0.6014 | -0.9003 | -0.0012 | 0.3671 | 0.068 | 0.0102 | 0.4217 | 0.085 | 0.2322 | 38.436 | 157.2097 | 5.4359 | 16 | 2.2144 | 0.4717 | -0.8749 | 1.5927 | -1.3415 | 0.3381 | 0.1338 | 0.4241 | 1.4946 | -0.3436 | -0.1084 | 0.4105 | -0.0177 | -0.1056 | -0.1122 | 0.4212 | 0.0939 | 0.0077 | 0.4141 | 0.1666 | 0.4357 | 29.4158 | 165.1569 | 9.5767 | 17 | 0.3926 | 0.2777 | 0.0597 | 0.2964 | -0.2023 | 0.2964 | -0.1261 | 0.0922 | -0.7335 | 0.1569 | 0.1867 | 1.145 | 0.296 | -0.3445 | -0.0008 | 0.4648 | -0.0331 | 0.0773 | 0.5015 | -0.0349 | 0.6328 | 10.2374 | 93.8671 | 24.254 | 18 | 2.2818 | -1.0199 | 0.7074 | 1.2429 | 0.8807 | 1.4981 | -0.0933 | -0.1156 | -0.3682 | 0.6213 | 0.0282 | -0.0279 | -0.0896 | 0.1165 | 0.0001 | 0.4782 | -0.0418 | 0.037 | 0.2855 | 0.0302 | 0.4825 | 22.7368 | 89.4905 | 30.6964 | 19 | 2.5639 | -0.2883 | 1.093 | 1.6784 | 0.2235 | 1.5015 | -0.1668 | 0.0347 | -0.3395 | 0.5086 | -0.0143 | 0.1802 | -0.0977 | -0.1512 | 0 | 0.428 | -0.0429 | 0.0851 | 0.293 | 0.0021 | 0.4737 | 19.2307 | 91.8603 | 27.1835 | 20 | 2.8128 | 1.2313 | 0.6085 | 1.5424 | -1.1602 | 2.2529 | -0.0276 | 0.217 | -0.1588 | -0.3472 | -0.0244 | -0.2256 | -0.3333 | 0.4216 | 0.0003 | 0.3376 | 0.0283 | 0.016 | 0.6343 | -0.1343 | 0.4733 | 12.8256 | 95.7643 | -1.7585 | 21 | 0.5226 | -0.2845 | -0.325 | 0.9106 | 0.0707 | 0.1901 | -0.1077 | 0.2026 | -0.6381 | -0.192 | 0.1706 | 0.5551 | -0.1338 | 0.5938 | 0.0685 | 0.4267 | 0.0197 | -0.0732 | 0.7975 | -0.2804 | 0.6096 | 8.4557 | 89.2853 | -4.8477 | 22 | 0.766 | 0.2085 | 0.0656 | -0.0248 | -0.0125 | 0.109 | -0.0815 | 0.0252 | -0.4487 | -0.0736 | 0.4041 | 0.0764 | 0.5074 | 0.3803 | 0.0007 | 0.444 | 0.0131 | -0.0077 | 0.6729 | -0.0606 | 0.4483 | 3.7486 | 92.394 | -0.8314 | 23 | 0.3914 | -0.3686 | 0.1969 | 0.6642 | -0.1393 | 0.724 | -0.0642 | 0.3101 | 0.0988 | 0.5206 | -0.2397 | -0.5444 | -0.1676 | 0.6046 | -0.0408 | 0.3622 | -0.1265 | -0.0468 | 0.6147 | 0.1463 | 0.6485 | 40.456 | 93.0749 | 21.7222 | 24 | 1.9025 | -1.719 | 0.4714 | 2.119 | -1.4156 | 1.8313 | 0.1027 | 0.4456 | -0.0623 | 0.0929 | -0.3427 | -0.3514 | -0.102 | 0.4203 | -0.0006 | 0.2724 | -0.0149 | 0.0273 | 0.503 | 0.0161 | 0.5649 | 37.0905 | 87.8988 | 20.0392 | 25 | 0.2027 | 0.7759 | -0.2055 | 2.2872 | -0.8052 | 0.8312 | -0.1249 | 1.1436 | -0.2616 | 0.0367 | -0.7409 | -0.5116 | 0.3488 | 0.0602 | -0.5705 | 0.2566 | 0.1267 | 0.1987 | 1.4212 | 0.0273 | 0.5769 | 37.6733 | 94.7771 | -0.1533 | 26 | 0.3732 | 0.6561 | -0.0326 | 0.7842 | -0.2061 | 3.6613 | 0.1095 | 0.6225 | 0.3379 | -0.1232 | -0.2213 | -0.0755 | -0.5841 | 0.3254 | -0.0003 | 0.5406 | -0.0388 | 0.0409 | 0.9129 | 0.1157 | 0.6311 | 21.26 | 105.6165 | -9.2125 | 27 | 0.1825 | -0.0396 | 0.017 | -0.0051 | 0.0323 | 0.0326 | 1.2074 | -0.3341 | -0.1648 | 0.7955 | 0.1168 | -0.98 | -0.4723 | 0.1522 | 0.0052 | 0.697 | -0.0001 | -0.1944 | 0.509 | 0.1422 | 0.8955 | 37.4249 | 83.8525 | 38.663 |
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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 3 through 22 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 23 through 82 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 83A through 116 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 117 through 142 )A0 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 143 through 182 )A0 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 183 through 210 )A0 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 1 through 25 )B0 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 26 through 38 )B0 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 39 through 61 )B0 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 62 through 90 )B0 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 91 through 101 )B0 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 102 through 113 )B0 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 114 through 128 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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