ソフトウェア | 名称 | 分類 |
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XDS | データ削減 | XSCALE | データスケーリング | PHASER | 位相決定 | PHENIX | モデル構築 | PHENIX | 精密化 |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 2ux8, chain A 解像度: 2.15→50 Å / SU ML: 0.15 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 19.19
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2025 | 1968 | 6.49 % |
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Rwork | 0.172 | - | - |
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obs | 0.1741 | 30327 | 99.9 % |
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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 |
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原子変位パラメータ | Biso max: 112.68 Å2 / Biso mean: 45.623 Å2 / Biso min: 19.36 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.15→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2233 | 0 | 44 | 176 | 2453 |
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Biso mean | - | - | 31.41 | 47.23 | - |
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残基数 | - | - | - | - | 290 |
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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 | 2361 | X-RAY DIFFRACTION | f_angle_d0.889 | 3215 | X-RAY DIFFRACTION | f_chiral_restr0.057 | 365 | X-RAY DIFFRACTION | f_plane_restr0.006 | 421 | X-RAY DIFFRACTION | f_dihedral_angle_d17.11 | 1445 | | | | | |
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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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2.15-2.2038 | 0.2438 | 119 | 0.2086 | 1999 | X-RAY DIFFRACTION | 100 | 2.2038-2.2634 | 0.2321 | 128 | 0.1886 | 1968 | X-RAY DIFFRACTION | 100 | 2.2634-2.33 | 0.2121 | 135 | 0.1783 | 1984 | X-RAY DIFFRACTION | 100 | 2.33-2.4052 | 0.2237 | 136 | 0.1806 | 1980 | X-RAY DIFFRACTION | 100 | 2.4052-2.4911 | 0.1899 | 144 | 0.1816 | 2004 | X-RAY DIFFRACTION | 100 | 2.4911-2.5909 | 0.2467 | 120 | 0.1824 | 1987 | X-RAY DIFFRACTION | 100 | 2.5909-2.7087 | 0.2112 | 144 | 0.1847 | 1984 | X-RAY DIFFRACTION | 100 | 2.7087-2.8515 | 0.2143 | 149 | 0.1923 | 1996 | X-RAY DIFFRACTION | 100 | 2.8515-3.0301 | 0.2212 | 132 | 0.1978 | 2037 | X-RAY DIFFRACTION | 100 | 3.0301-3.264 | 0.2199 | 150 | 0.1883 | 2012 | X-RAY DIFFRACTION | 100 | 3.264-3.5923 | 0.1954 | 156 | 0.1712 | 2005 | X-RAY DIFFRACTION | 100 | 3.5923-4.1117 | 0.1754 | 151 | 0.1479 | 2056 | X-RAY DIFFRACTION | 100 | 4.1117-5.1788 | 0.1722 | 153 | 0.1376 | 2080 | X-RAY DIFFRACTION | 100 | 5.1788-50 | 0.2157 | 151 | 0.18 | 2267 | 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 | 2.4063 | -0.068 | 0.6515 | 2.087 | 0.6063 | 3.2611 | -0.0576 | -0.1822 | 0.153 | 0.088 | 0.1752 | -0.0345 | -0.5658 | -0.0565 | -0.0932 | 0.4345 | 0.0819 | 0.0293 | 0.1378 | -0.0293 | 0.2181 | 41.3381 | 15.45 | 138.3296 | 2 | 4.4001 | 1.0375 | -0.8395 | 2.191 | -0.5119 | 2.3814 | -0.2263 | 0.3627 | -0.2051 | -0.1991 | 0.1033 | -0.1476 | 0.1508 | 0.3464 | 0.1745 | 0.4017 | 0.0682 | 0.006 | 0.2151 | -0.0203 | 0.2264 | 50.4229 | 7.1641 | 133.1889 | 3 | 2.6566 | -0.3145 | -1.5176 | 1.1821 | 0.0283 | 2.2426 | -0.0933 | -0.2021 | -0.0464 | 0.2066 | 0.1364 | 0.0379 | -0.2438 | 0.2571 | -0.0109 | 0.3795 | 0.0706 | -0.0416 | 0.1894 | -0.0142 | 0.2097 | 43.2453 | 10.6073 | 143.3267 | 4 | 2.2846 | -1.5112 | -0.8582 | 2.2615 | 0.2713 | 0.9661 | 0.0062 | -0.3646 | 0.591 | 0.2419 | 0.1339 | -0.0234 | -0.9105 | 0.0835 | -0.0266 | 0.8315 | 0.3071 | 0.0816 | 0.2299 | -0.0808 | 0.3786 | 31.879 | 26.212 | 154.0692 | 5 | 4.4517 | -0.9941 | -0.1782 | 4.7405 | 0.6918 | 1.2907 | -0.0839 | -0.2512 | -0.2252 | 0.2539 | 0.1076 | 0.6712 | -0.3338 | -0.4167 | 0.0102 | 0.5103 | 0.1959 | 0.0571 | 0.3042 | 0.0266 | 0.3299 | 28.612 | 14.4385 | 154.4332 | 6 | 0.4794 | -0.3045 | -0.3456 | 1.2641 | 0.6801 | 0.8326 | 0.13 | -0.1421 | 0.2813 | 0.1957 | 0.1672 | -0.0796 | -0.4837 | 0.1147 | 0.0506 | 1.0793 | 0.0956 | 0.0582 | 0.023 | -0.0719 | 0.4002 | 40.6789 | 29.0812 | 136.0169 | 7 | 3.9709 | 2.2035 | 1.8839 | 6.134 | 0.3997 | 3.3438 | 0.4928 | -0.4165 | 0.3901 | 0.2324 | -0.0826 | 0.2914 | -0.6411 | 0.2303 | -0.2113 | 1.2787 | -0.3809 | 0.1431 | 0.3616 | -0.1535 | 0.7068 | 49.6045 | 36.9311 | 125.0489 |
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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 0 through 47 )A0 - 47 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 48 through 83 )A48 - 83 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 84 through 141 )A84 - 141 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 142 through 206 )A142 - 206 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 207 through 248 )A207 - 248 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 249 through 271 )A249 - 271 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 272 through 289 )A272 - 289 | | | | | | | | | | | | | | |
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