ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.6_289精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | HKL-3000 | | 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: 6CB6 解像度: 1.6→30.289 Å / SU ML: 0.18 / 交差検証法: NONE / σ(F): 0.1 / 位相誤差: 17.68
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1895 | 3314 | 10.02 % |
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Rwork | 0.1661 | - | - |
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obs | 0.1686 | 33073 | 94.81 % |
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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 / Bsol: 40.732 Å2 / ksol: 0.351 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.6744 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 1.6744 Å2 | 0 Å2 |
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3- | - | - | -3.3487 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→30.289 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 956 | 0 | 1 | 148 | 1105 |
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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 | 991 | X-RAY DIFFRACTION | f_angle_d0.904 | 1346 | X-RAY DIFFRACTION | f_dihedral_angle_d14.352 | 363 | X-RAY DIFFRACTION | f_chiral_restr0.064 | 161 | X-RAY DIFFRACTION | f_plane_restr0.005 | 166 | | | | | |
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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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1.5972-1.6542 | 0.212 | 249 | 0.1807 | 2211 | X-RAY DIFFRACTION | 71 | 1.6542-1.7205 | 0.1946 | 316 | 0.1695 | 2848 | X-RAY DIFFRACTION | 91 | 1.7205-1.7988 | 0.222 | 322 | 0.1655 | 3008 | X-RAY DIFFRACTION | 96 | 1.7988-1.8936 | 0.2141 | 339 | 0.1643 | 3048 | X-RAY DIFFRACTION | 97 | 1.8936-2.0122 | 0.1925 | 332 | 0.1584 | 3070 | X-RAY DIFFRACTION | 98 | 2.0122-2.1675 | 0.1695 | 353 | 0.1492 | 3109 | X-RAY DIFFRACTION | 99 | 2.1675-2.3856 | 0.2001 | 341 | 0.1545 | 3113 | X-RAY DIFFRACTION | 99 | 2.3856-2.7306 | 0.1691 | 352 | 0.1645 | 3101 | X-RAY DIFFRACTION | 99 | 2.7306-3.4395 | 0.2044 | 346 | 0.178 | 3142 | X-RAY DIFFRACTION | 100 | 3.4395-30.2944 | 0.1691 | 364 | 0.1562 | 3109 | X-RAY DIFFRACTION | 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 | 5.8942 | -1.1586 | -1.9533 | 1.4419 | -2.9507 | 9.7638 | -0.307 | -0.1209 | -0.2076 | -0.4088 | 0.1906 | 0.2064 | 1.0983 | 0.027 | 0.1288 | 0.1596 | 0.0033 | 0.015 | 0.1012 | 0.0039 | 0.1373 | 3.2865 | -27.8708 | 16.2637 | 2 | 0.2675 | 0.0435 | -0.1054 | 3.3465 | -1.6103 | 1.1576 | -0.0071 | -0.0303 | 0.1574 | 0.1675 | -0.0056 | 0.4682 | -0.2075 | -0.114 | 0.0166 | 0.1508 | 0.0018 | -0.0066 | 0.1332 | -0.0023 | 0.181 | 2.081 | -20.1952 | 11.0411 | 3 | 3.147 | -1.1288 | 1.7881 | 0.7763 | -0.6621 | 6.4938 | 0.0231 | 0.0127 | 0.5329 | 0.0945 | -0.2329 | 0.1538 | -0.3164 | -0.5065 | 0.1622 | 0.1804 | 0.0404 | -0.0133 | 0.1708 | -0.0051 | 0.1834 | 0.0806 | -13.3805 | 3.8681 | 4 | 3.2328 | -1.1648 | 1.7864 | 2.1791 | -4.3076 | 8.7128 | -0.035 | 0.2503 | 0.6715 | -0.17 | -0.2107 | 0.2843 | -0.7961 | -0.39 | 0.1312 | 0.293 | 0.0853 | -0.0631 | 0.2213 | 0.0405 | 0.2339 | -2.6885 | -11.8037 | -2.9457 | 5 | 0.033 | -0.0342 | -0.2325 | 3.7638 | -1.1238 | 3.8908 | -0.0278 | -0.0418 | -0.3647 | 0.0756 | 0.0917 | 0.5038 | 0.1853 | -0.4715 | -0.0283 | 0.141 | -0.0158 | -0.0129 | 0.1645 | -0.022 | 0.2099 | 1.1085 | -28.2745 | 3.5366 | 6 | 5.0205 | -0.383 | -0.0211 | 0.4317 | 0.9675 | 2.5931 | -0.2102 | -0.1163 | -0.313 | -0.0343 | 0.0458 | 0.2612 | 0.2562 | -0.1262 | 0.0727 | 0.1371 | 0.0075 | -0.0288 | 0.0961 | -0.0039 | 0.1521 | 13.3639 | -28.5467 | 4.8902 | 7 | 0.4982 | 0.6565 | 0.6093 | 2.2873 | -0.034 | 1.1682 | 0.0535 | -0.0687 | 0.0288 | 0.0954 | 0.0455 | -0.212 | -0.1915 | 0.2214 | -0.0457 | 0.1365 | -0.0133 | 0.0177 | 0.1588 | -0.0121 | 0.1444 | 22.0925 | -21.7198 | 9.2889 | 8 | 3.3161 | -0.4844 | -0.4134 | 0.9953 | -1.8015 | 4.0298 | -0.0288 | 0.0937 | 0.5298 | 0.169 | -0.1292 | -0.4878 | -0.9098 | 0.5138 | 0.0548 | 0.2026 | -0.0627 | 0.0022 | 0.1133 | -0.0019 | 0.1689 | 21.3287 | -13.4708 | 13.4024 | 9 | 2.1707 | 0.5024 | -0.5445 | 1.2774 | -0.3344 | 0.4935 | 0.1347 | 0.2601 | 0.0373 | -0.1173 | -0.0492 | -0.0082 | -0.0534 | 0.048 | -0.0711 | 0.1638 | -0.0129 | 0.0231 | 0.1387 | -0.003 | 0.1451 | 16.9004 | -14.477 | 5.505 | 10 | 1.4222 | -0.1119 | 0.2028 | 0.102 | 0.315 | 1.1292 | 0.1147 | -0.0242 | -0.0727 | -0.0984 | -0.0791 | 0.0033 | -0.2538 | -0.0871 | -0.0303 | 0.1705 | 0.0151 | -0.0045 | 0.1255 | -0.0182 | 0.1233 | 11.148 | -19.5432 | -0.9932 | 11 | 2.75 | -0.5776 | 1.7288 | 0.1767 | -0.3787 | 1.9377 | 0.0381 | 0.2397 | -0.1623 | 0.024 | -0.0959 | 0.2221 | -0.3797 | -0.1604 | 0.0563 | 0.1627 | 0.0088 | -0.0278 | 0.1825 | -0.0259 | 0.1958 | 2.4852 | -21.6003 | -0.5358 | 12 | 1.4417 | -0.6113 | -1.1589 | 1.7229 | 1.4755 | 1.5906 | 0.2768 | 0.5272 | -0.091 | -0.0281 | -0.2031 | -0.1643 | -0.3721 | -0.2809 | 0.0185 | 0.2587 | 0.0304 | -0.059 | 0.2288 | -0.0514 | 0.1147 | 4.157 | -20.2006 | -6.6778 | 13 | 0.3091 | -0.6208 | -0.0788 | 5.6292 | 3.0827 | 1.9487 | 0.1098 | 0.0512 | 0.0668 | -0.6861 | 0.0222 | -0.2922 | -0.6858 | -0.0338 | -0.1183 | 0.2401 | 0.0177 | 0.0151 | 0.0718 | 0.0065 | 0.1094 | 8.731 | -7.7743 | 5.4912 | 14 | 0.3774 | -0.1959 | 0.0369 | 1.4967 | 0.8582 | 0.6153 | 0.0753 | -0.2176 | 0.211 | 0.3266 | -0.1135 | 0.1903 | -0.0201 | 0.1114 | -0.0124 | 0.1547 | 0.0107 | 0.0031 | 0.0787 | -0.0186 | 0.1289 | 7.9669 | -7.723 | 13.8771 | 15 | 1.5476 | -0.2196 | 0.6633 | 0.7718 | -0.8619 | 2.0765 | 0.0459 | -0.174 | 0.1403 | -0.0431 | -0.1609 | 0.0689 | -0.1764 | -0.1382 | 0.0927 | 0.1481 | 0.0038 | -0.0014 | 0.0852 | 0.0047 | 0.1085 | 11.1142 | -16.6285 | 13.177 | 16 | 0.5252 | 0.4749 | -0.457 | 0.7386 | -1.0036 | 1.9821 | 0.0123 | 0.0301 | 0.0756 | 0.1142 | 0.0742 | 0.3305 | -0.015 | -0.233 | -0.0637 | 0.1476 | -0.0013 | -0.0036 | 0.0993 | -0.0016 | 0.1159 | 12.8542 | -25.7297 | 13.5303 | 17 | 4.6235 | -4.4902 | -0.35 | 8.3743 | 0.5154 | 0.9415 | 0.0638 | -0.099 | -0.6635 | -0.1122 | -0.1761 | 0.2247 | 0.1648 | 0.6282 | 0.0516 | 0.2527 | 0.0398 | 0.0303 | 0.1693 | 0.0275 | 0.1339 | 17.1679 | -33.9668 | 13.257 |
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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 1:5)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 6:13)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 14:19)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 20:27)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 28:36)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 37:44)7 | X-RAY DIFFRACTION | 7 | (chain A and resid 45:55)8 | X-RAY DIFFRACTION | 8 | (chain A and resid 56:61)9 | X-RAY DIFFRACTION | 9 | (chain A and resid 62:67)10 | X-RAY DIFFRACTION | 10 | (chain A and resid 68:73)11 | X-RAY DIFFRACTION | 11 | (chain A and resid 74:77)12 | X-RAY DIFFRACTION | 12 | (chain A and resid 78:83)13 | X-RAY DIFFRACTION | 13 | (chain A and resid 84:94)14 | X-RAY DIFFRACTION | 14 | (chain A and resid 95:99)15 | X-RAY DIFFRACTION | 15 | (chain A and resid 100:106)16 | X-RAY DIFFRACTION | 16 | (chain A and resid 107:112)17 | X-RAY DIFFRACTION | 17 | (chain A and resid 113:117) | | | | | | | | | | | | | | | | |
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