ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.10.1-2155_1496) | 精密化 | HKL-3000 | | データ削減 | HKL-3000 | | 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: 5SUJ 解像度: 2.008→36.025 Å / SU ML: 0.2 / 交差検証法: FREE R-VALUE / σ(F): 0.05 / 位相誤差: 21.25 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2104 | 1943 | 3.85 % | Random selection |
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Rwork | 0.1739 | - | - | - |
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obs | 0.1753 | 50531 | 93.03 % | - |
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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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精密化ステップ | サイクル: LAST / 解像度: 2.008→36.025 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6048 | 0 | 0 | 465 | 6513 |
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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_d0.005 | 6191 | X-RAY DIFFRACTION | f_angle_d0.702 | 8358 | X-RAY DIFFRACTION | f_dihedral_angle_d15.936 | 2364 | X-RAY DIFFRACTION | f_chiral_restr0.049 | 915 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1085 | | | | | |
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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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2.0083-2.0585 | 0.2469 | 114 | 0.209 | 2618 | X-RAY DIFFRACTION | 71 | 2.0585-2.1142 | 0.256 | 134 | 0.2087 | 3203 | X-RAY DIFFRACTION | 86 | 2.1142-2.1764 | 0.2498 | 135 | 0.1961 | 3349 | X-RAY DIFFRACTION | 90 | 2.1764-2.2466 | 0.2379 | 130 | 0.1916 | 3442 | X-RAY DIFFRACTION | 92 | 2.2466-2.3269 | 0.202 | 143 | 0.1826 | 3471 | X-RAY DIFFRACTION | 93 | 2.3269-2.42 | 0.2051 | 129 | 0.1836 | 3535 | X-RAY DIFFRACTION | 95 | 2.42-2.5301 | 0.2425 | 142 | 0.1851 | 3538 | X-RAY DIFFRACTION | 95 | 2.5301-2.6635 | 0.2431 | 138 | 0.1879 | 3583 | X-RAY DIFFRACTION | 96 | 2.6635-2.8303 | 0.2376 | 146 | 0.1894 | 3626 | X-RAY DIFFRACTION | 97 | 2.8303-3.0487 | 0.2532 | 144 | 0.19 | 3663 | X-RAY DIFFRACTION | 98 | 3.0487-3.3553 | 0.1981 | 149 | 0.176 | 3652 | X-RAY DIFFRACTION | 98 | 3.3553-3.8404 | 0.2027 | 145 | 0.1596 | 3690 | X-RAY DIFFRACTION | 98 | 3.8404-4.8366 | 0.1496 | 149 | 0.1387 | 3672 | X-RAY DIFFRACTION | 99 | 4.8366-36.0309 | 0.2015 | 145 | 0.1645 | 3546 | X-RAY DIFFRACTION | 95 |
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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 | 4.296 | -0.4951 | 0.0268 | 2.1606 | 0.7564 | 6.1202 | 0.3779 | 0.6784 | 0.2644 | -0.8143 | -0.2964 | 0.2266 | -0.8436 | -0.6229 | 0.0373 | 0.2625 | 0.0956 | -0.0228 | 0.2223 | 0.036 | 0.1866 | 19.6495 | 66.4062 | -20.1762 | 2 | 8.5264 | 3.7324 | -5.7818 | 2.9985 | -2.696 | 3.9476 | 0.0339 | 0.101 | -0.0743 | -0.1636 | -0.0263 | 0.0222 | -0.1219 | -0.1315 | -0.0295 | 0.1129 | 0.025 | -0.0423 | 0.117 | -0.0112 | 0.1237 | 7.1729 | 65.309 | -2.2808 | 3 | 7.0066 | -5.7141 | -5.4559 | 7.3953 | 5.2645 | 4.8572 | -0.0502 | -0.7002 | 0.4044 | -0.0646 | 0.298 | -0.2704 | -0.6384 | 0.8392 | -0.2857 | 0.2326 | -0.0212 | -0.0054 | 0.253 | 0.0163 | 0.2043 | 4.2115 | 68.6784 | 19.0089 | 4 | 2.8831 | -1.7244 | -4.553 | 2.4086 | 2.1341 | 7.1207 | 0.4361 | -0.7697 | 0.2539 | 0.2795 | 0.2047 | -0.7339 | -0.4656 | 1.1993 | -0.6003 | 0.1936 | -0.0838 | -0.0001 | 0.3029 | -0.0474 | 0.2389 | 10.6986 | 70.2812 | 9.3474 | 5 | 0.5609 | 1.1982 | 1.2152 | 6.8893 | 2.6597 | 2.7368 | 0.0982 | -0.426 | -0.1376 | -0.0652 | 0.0237 | 0.6287 | 0.0335 | -0.6462 | 0.0962 | 0.0878 | 0.0049 | 0.0065 | 0.2392 | 0.0134 | 0.1789 | 18.9731 | 56.1051 | -7.0302 | 6 | 6.5018 | -2.0745 | 4.1585 | 4.8375 | -1.6092 | 3.1103 | 0.3561 | 0.0558 | -1.4393 | -0.2218 | 0.0384 | 0.7892 | 0.4353 | -0.2257 | -0.3388 | 0.2374 | -0.0148 | -0.0078 | 0.1733 | 0.0035 | 0.2566 | 23.4046 | 46.7767 | -14.3465 | 7 | 3.6793 | -1.6723 | 1.6354 | 2.2299 | -0.7762 | 4.5927 | 0.1962 | -0.1756 | -0.3835 | -0.0932 | 0.0333 | 0.1255 | 0.2174 | -0.0386 | -0.1482 | 0.139 | 0.0268 | -0.0038 | 0.0977 | -0.0189 | 0.1478 | 32.3503 | 49.4655 | -13.348 | 8 | 4.9174 | 0.6195 | 1.8073 | 5.1618 | 0.8959 | 4.7532 | 0.0564 | 0.2388 | -0.5156 | 0.0954 | 0.0279 | -0.033 | 0.3371 | 0.1109 | -0.0344 | 0.206 | -0.0519 | 0.0023 | 0.1294 | -0.0188 | 0.233 | 41.7678 | 35.8685 | 20.7456 | 9 | 5.654 | -1.5453 | 1.8785 | 3.2153 | -0.052 | 5.0196 | -0.0541 | 1.8224 | 0.5107 | -2.4253 | -0.5483 | 1.5476 | 0.5301 | -0.4099 | 0.5445 | 0.8213 | 0.0122 | -0.2019 | 0.6757 | -0.1515 | 0.563 | 40.6759 | 32.496 | 5.168 | 10 | 4.9533 | -1.1884 | 1.6385 | 4.1321 | 0.6287 | 4.2787 | 0.0572 | 0.2049 | 0.0049 | -0.2731 | -0.0628 | -0.2407 | -0.2513 | 0.1948 | 0.1524 | 0.0421 | -0.0059 | 0.0236 | 0.059 | -0.0498 | 0.1201 | 30.9583 | 55.0416 | -15.5119 | 11 | 2.9662 | -0.7482 | -1.5446 | 2.5276 | 2.8494 | 5.7556 | 0.0813 | -0.1828 | 0.2762 | -0.2608 | -0.1181 | -0.2506 | -0.3744 | -0.0826 | -0.1195 | 0.1155 | 0.0301 | 0.0317 | 0.1513 | -0.0197 | 0.0622 | 27.9945 | 64.0936 | -8.6838 | 12 | 5.0144 | -3.0708 | 3.7257 | 6.0623 | -5.9797 | 7.8392 | 0.039 | -0.084 | 0.5552 | -0.3584 | -0.3077 | -0.9601 | 0.2754 | 0.4748 | 0.2103 | 0.1198 | 0.0253 | 0.0355 | 0.171 | -0.0436 | 0.1929 | 41.4202 | 56.4401 | -11.5264 | 13 | 3.9191 | 0.4734 | 2.168 | 2.8361 | 0.4837 | 3.3449 | -0.0263 | -0.3674 | 0.0929 | 0.3175 | -0.0496 | -0.1497 | -0.1362 | 0.1281 | 0.0628 | 0.0741 | -0.0035 | 0.0248 | 0.1885 | 0.0029 | 0.1102 | 36.3128 | 56.9561 | -3.0625 | 14 | 4.1441 | -4.7509 | -2.6806 | 7.912 | 6.0748 | 6.4379 | 0.3711 | 0.5477 | -0.227 | -0.397 | -0.3875 | 0.3806 | -0.2314 | -0.456 | 0.6795 | 0.1807 | 0.0429 | -0.0677 | 0.179 | -0.001 | 0.2145 | 8.0985 | 64.4674 | -17.3348 | 15 | 6.7253 | -2.0062 | 0.3208 | 7.9561 | -5.8059 | 8.6371 | -0.0851 | 0.1003 | 1.0499 | -0.0106 | -0.0157 | -0.584 | -0.5694 | 0.3906 | 0.1271 | 0.2181 | 0.0077 | 0.047 | 0.1091 | -0.0092 | 0.2484 | 8.8283 | 78.0374 | -8.5139 | 16 | 4.6096 | 0.0883 | -2.2059 | 7.083 | -1.173 | 6.1729 | 0.4638 | -0.6055 | 0.1346 | 0.5215 | -0.0404 | 0.5527 | -0.4147 | -0.8169 | -0.3861 | 0.1315 | -0.0179 | 0.035 | 0.3445 | -0.0233 | 0.1609 | -0.2736 | 69.4501 | 9.0537 | 17 | 7.1161 | -0.4012 | -3.4073 | 3.0947 | 0.749 | 3.3469 | -0.0492 | -0.5489 | -0.0027 | 0.3264 | 0.1041 | 0.0987 | -0.0986 | 0.2815 | -0.0627 | 0.1265 | 0.0167 | -0.0023 | 0.0985 | 0.0092 | 0.0966 | 8.7485 | 85.9698 | -20.3002 | 18 | 3.1345 | 2.7837 | -4.7522 | 5.0922 | -3.7808 | 7.9069 | 0.1849 | 0.1988 | -0.0256 | -0.1793 | -0.0158 | -0.2808 | -0.1512 | 0.1492 | -0.196 | 0.1322 | 0.0083 | 0.0325 | 0.1866 | 0.0017 | 0.1427 | 26.682 | 91.0356 | -46.5266 | 19 | 8.1744 | -2.4489 | -3.208 | 0.7889 | 0.5254 | 2.506 | -0.166 | -0.0257 | 0.2313 | -0.0315 | 0.076 | -0.1719 | -0.1014 | 0.166 | 0.033 | 0.2126 | -0.0222 | 0.0195 | 0.1305 | -0.056 | 0.178 | 14.6607 | 94.048 | -35.1483 | 20 | 6.6111 | -4.1478 | 2.4479 | 6.4153 | -1.6987 | 4.4374 | 0.0524 | 0.6684 | -0.1841 | -0.6195 | -0.209 | 0.3213 | 0.565 | 0.165 | 0.1043 | 0.2257 | -0.041 | -0.0013 | 0.1794 | -0.0488 | 0.2374 | -5.7245 | 85.6525 | -31.3912 | 21 | 3.7111 | -1.9965 | 0.3805 | 5.818 | -2.5592 | 3.2897 | 0.0794 | -0.2036 | 0.0239 | -0.0643 | 0.2591 | 0.9672 | -0.0588 | -0.3093 | -0.2277 | 0.1049 | -0.0191 | 0.0181 | 0.1434 | -0.0398 | 0.2867 | -12.1881 | 94.7892 | -22.6131 | 22 | 1.579 | -0.6505 | 0.7494 | 0.4164 | -0.5765 | 0.9283 | -0.3302 | 0.8487 | -0.43 | -1.3774 | 0.5554 | -0.3305 | 0.3134 | 0.6394 | -0.0808 | 0.9148 | -0.2449 | -0.0374 | 0.4869 | -0.0941 | 0.3368 | -8.3685 | 115.1367 | -52.7256 | 23 | 6.126 | 1.6054 | 2.0693 | 2.7757 | 0.379 | 8.9052 | -0.5593 | 0.9271 | -0.9727 | -1.6688 | 0.6196 | -0.356 | 0.3632 | 0.7401 | -0.518 | 0.9969 | -0.431 | -0.0663 | 0.6001 | -0.2971 | 0.3069 | -7.6852 | 111.4589 | -57.5316 | 24 | 0.409 | -0.0798 | -0.2612 | 0.128 | 0.0039 | 0.1808 | -0.4711 | 0.57 | 0.2919 | -0.5838 | 0.0186 | 0.2483 | -0.3087 | -0.1508 | -0.1213 | 1.5057 | -0.5558 | -1.2998 | 0.9512 | 0.1752 | 0.9498 | -20.6298 | 117.0244 | -61.9504 | 25 | 3.6716 | 2.6488 | -1.1129 | 2.027 | -0.948 | 4.255 | -0.4754 | 0.9634 | 1.8132 | -1.5567 | 0.906 | 1.7864 | -0.6374 | -0.859 | -0.226 | 0.8443 | -0.278 | -0.3197 | 0.4677 | 0.2334 | 0.9742 | -14.4226 | 129.3401 | -52.9571 | 26 | 3.4489 | -2.8495 | 4.2933 | 4.7882 | -5.324 | 6.8875 | 0.0277 | 0.1915 | 0.1775 | -0.4923 | 0.2214 | 0.9346 | 0.0808 | -0.2162 | -0.356 | 0.3099 | -0.0342 | -0.1405 | 0.2067 | 0.036 | 0.4896 | -12.8289 | 107.3843 | -41.3257 | 27 | 2.8246 | -2.1996 | 3.1154 | 4.6241 | -3.6525 | 3.9624 | -0.6982 | -1.4539 | -0.3856 | 1.8412 | -0.0749 | 0.6634 | -0.2094 | -0.5931 | -0.149 | 0.4614 | -0.0332 | 0.2493 | 0.4291 | 0.1015 | 0.3659 | -8.2837 | 90.6422 | -9.5142 | 28 | 3.1276 | -1.465 | -0.3889 | 2.716 | -0.1573 | 1.294 | -0.0516 | -0.1627 | 0.0817 | 0.1202 | 0.0096 | 0.1 | -0.1454 | 0.0394 | 0.0498 | 0.1119 | -0.0255 | 0.0151 | 0.0706 | -0.0566 | 0.1149 | -0.8102 | 103.462 | -22.8071 | 29 | 2.9839 | -1.5694 | 0.7512 | 3.0783 | -0.3639 | 1.8227 | -0.0699 | -0.0075 | 0.4096 | -0.1161 | -0.0123 | -0.0472 | -0.2127 | 0.0464 | 0.0995 | 0.1356 | 0.0042 | 0.0533 | 0.0978 | -0.0601 | 0.13 | -1.7991 | 102.3066 | -27.0611 | 30 | 7.0696 | -2.9022 | -3.7244 | 1.425 | 1.5747 | 6.1186 | -0.2703 | -0.0718 | -0.547 | 0.0258 | -0.0503 | 0.1663 | 0.5157 | 0.1601 | 0.2655 | 0.2041 | 0.0109 | -0.0041 | 0.0928 | 0.0367 | 0.2006 | 13.2652 | 77.2202 | -24.461 | 31 | 2.0191 | 0.6082 | -1.0041 | 3.9155 | -1.8434 | 6.3511 | -0.0298 | -0.3295 | 0.0172 | 0.0024 | 0.0702 | -0.3499 | 0.2259 | 0.8592 | 0.0076 | 0.0631 | 0.0353 | -0.0064 | 0.2493 | -0.0077 | 0.1507 | 25.6833 | 84.8466 | -32.0059 | 32 | 6.0396 | -4.7926 | 6.6743 | 9.3658 | -3.1373 | 8.206 | -0.9862 | 1.2542 | -1.5148 | -1.4684 | -0.1423 | 0.0669 | 1.8333 | 0.2799 | 0.9622 | 0.7655 | -0.1402 | 0.2843 | 0.3911 | -0.0796 | 0.4847 | 29.2778 | 84.1596 | -53.7248 |
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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 A and resid 7:22)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 23:41)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 42:56)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 57:71)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 72:83)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 84:105)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 106:129)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 130:217)9 | X-RAY DIFFRACTION | 9 | (chain A and resid 218:225)10 | X-RAY DIFFRACTION | 10 | (chain A and resid 226:245)11 | X-RAY DIFFRACTION | 11 | (chain A and resid 246:272)12 | X-RAY DIFFRACTION | 12 | (chain A and resid 273:292)13 | X-RAY DIFFRACTION | 13 | (chain A and resid 293:334)14 | X-RAY DIFFRACTION | 14 | (chain A and resid 335:353)15 | X-RAY DIFFRACTION | 15 | (chain A and resid 354:364)16 | X-RAY DIFFRACTION | 16 | (chain A and resid 365:384)17 | X-RAY DIFFRACTION | 17 | (chain B and resid 7:33)18 | X-RAY DIFFRACTION | 18 | (chain B and | | | | | | | | | | | | | | | | | |
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