ソフトウェア | 名称 | バージョン | 分類 |
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XDS | 20200417 | データ削減 | XSCALE | 20200417 | データスケーリング | PHASER | 2.7.15位相決定 | PHENIX | 1.19.2精密化 | PDB_EXTRACT | 3.27 | データ抽出 | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4EE9 解像度: 1.49→15.57 Å / SU ML: 0.15 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 19.38 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1933 | 5642 | 5 % |
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Rwork | 0.1741 | 107185 | - |
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obs | 0.1751 | 112827 | 99.37 % |
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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: 146.6 Å2 / Biso mean: 30.5152 Å2 / Biso min: 12.13 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.49→15.57 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5108 | 0 | 20 | 877 | 6005 |
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Biso mean | - | - | 37.83 | 39.86 | - |
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残基数 | - | - | - | - | 638 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.49-1.51 | 0.3323 | 159 | 0.2947 | 3013 | 3172 | 85 | 1.51-1.53 | 0.2912 | 187 | 0.2658 | 3558 | 3745 | 100 | 1.53-1.55 | 0.2686 | 188 | 0.2502 | 3566 | 3754 | 100 | 1.55-1.57 | 0.2572 | 183 | 0.2266 | 3487 | 3670 | 100 | 1.57-1.59 | 0.2355 | 189 | 0.2209 | 3580 | 3769 | 100 | 1.59-1.61 | 0.2768 | 187 | 0.2151 | 3565 | 3752 | 100 | 1.61-1.63 | 0.2484 | 186 | 0.2051 | 3536 | 3722 | 100 | 1.63-1.65 | 0.2082 | 188 | 0.198 | 3557 | 3745 | 100 | 1.65-1.68 | 0.2067 | 187 | 0.1962 | 3558 | 3745 | 100 | 1.68-1.71 | 0.2295 | 188 | 0.187 | 3569 | 3757 | 100 | 1.71-1.74 | 0.2409 | 187 | 0.192 | 3552 | 3739 | 100 | 1.74-1.77 | 0.2217 | 188 | 0.1895 | 3570 | 3758 | 100 | 1.77-1.8 | 0.2074 | 187 | 0.1896 | 3570 | 3757 | 100 | 1.8-1.84 | 0.214 | 189 | 0.1929 | 3581 | 3770 | 100 | 1.84-1.88 | 0.2304 | 186 | 0.1947 | 3541 | 3727 | 100 | 1.88-1.92 | 0.2114 | 189 | 0.1899 | 3587 | 3776 | 100 | 1.92-1.97 | 0.2274 | 187 | 0.1918 | 3551 | 3738 | 100 | 1.97-2.02 | 0.2145 | 191 | 0.1945 | 3628 | 3819 | 100 | 2.02-2.08 | 0.2186 | 187 | 0.184 | 3556 | 3743 | 100 | 2.08-2.15 | 0.1984 | 188 | 0.1769 | 3579 | 3767 | 100 | 2.15-2.23 | 0.2154 | 190 | 0.1762 | 3606 | 3796 | 100 | 2.23-2.32 | 0.1915 | 190 | 0.18 | 3596 | 3786 | 100 | 2.32-2.42 | 0.1786 | 188 | 0.1709 | 3589 | 3777 | 100 | 2.42-2.55 | 0.2108 | 190 | 0.1787 | 3611 | 3801 | 100 | 2.55-2.71 | 0.1848 | 191 | 0.1739 | 3618 | 3809 | 100 | 2.71-2.92 | 0.2066 | 190 | 0.1807 | 3622 | 3812 | 100 | 2.92-3.21 | 0.1809 | 192 | 0.1679 | 3644 | 3836 | 100 | 3.21-3.66 | 0.1738 | 193 | 0.1652 | 3669 | 3862 | 100 | 3.67-4.6 | 0.1478 | 196 | 0.1426 | 3713 | 3909 | 100 | 4.6-15.57 | 0.1735 | 201 | 0.1531 | 3813 | 4014 | 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 | 0.6864 | 0.1438 | 0.3384 | 0.3414 | -0.3367 | 0.9426 | 0.0588 | -0.0115 | -0.1194 | 0.0773 | -0.0356 | -0.027 | -0.0428 | 0.262 | 0.056 | 0.123 | -0.0017 | -0.034 | 0.2266 | 0.0026 | 0.1985 | -37.0342 | 107.6486 | 32.5416 | 2 | 0.4308 | 0.1349 | 0.5977 | 0.7244 | 0.0803 | 1.3578 | -0.0002 | 0.0174 | 0.0599 | 0.0017 | -0.0164 | 0.0156 | -0.1647 | 0.0912 | 0 | 0.1273 | -0.0212 | 0.0014 | 0.1652 | 0.0136 | 0.1753 | -45.4581 | 114.665 | 25.4968 | 3 | 0.1366 | 0.071 | 0.1223 | 0.134 | 0.093 | 0.1091 | 0.0362 | 0.1432 | -0.001 | -0.1409 | 0.0261 | 0.1902 | -0.0268 | -0.1406 | 0.0034 | 0.14 | 0.0007 | -0.0351 | 0.228 | 0.0309 | 0.2112 | -56.7619 | 108.9811 | 16.8029 | 4 | 0.0404 | -0.1237 | -0.0199 | 0.271 | 0.0965 | 0.0842 | 0.091 | -0.0433 | -0.0884 | 0.0303 | 0.0858 | 0.1149 | 0.2511 | -0.3908 | 0.0057 | 0.2623 | -0.0781 | -0.0773 | 0.2262 | 0.0328 | 0.2522 | -58.425 | 92.1647 | 28.1357 | 5 | 0.542 | 0.2231 | -0.3716 | 0.1682 | -0.1662 | 0.344 | 0.1627 | -0.044 | -0.2196 | -0.0213 | -0.1164 | -0.0853 | 0.4483 | 0.2255 | 0.0275 | 0.2768 | 0.0121 | -0.093 | 0.1867 | 0.0256 | 0.2637 | -45.9685 | 92.2108 | 30.0654 | 6 | 0.2358 | 0.1471 | -0.0133 | 0.0834 | -0.018 | 0.048 | 0.0612 | 0.2415 | -0.299 | -0.166 | 0.0438 | -0.3816 | 0.4103 | 0.07 | 0.0037 | 0.3436 | 0.0868 | -0.0608 | 0.3062 | -0.0752 | 0.3693 | -43.6187 | 91.253 | 17.42 | 7 | 0.0551 | -0.0258 | -0.1106 | 0.257 | -0.0099 | 0.6325 | 0.1377 | 0.0476 | 0.1103 | 0.1128 | 0.012 | 0.1868 | -0.5082 | -0.1483 | -0.0078 | 0.2686 | 0.042 | 0.0836 | 0.2242 | 0.0524 | 0.2441 | -56.7246 | 108.4746 | 58.1224 | 8 | 0.8377 | -0.0489 | -0.0968 | 1.0147 | -0.3208 | 1.3027 | 0.0507 | 0.0343 | -0.0812 | -0.0628 | -0.0418 | 0.1156 | 0.097 | 0.0437 | 0 | 0.2085 | -0.0026 | 0.0468 | 0.1625 | -0.0254 | 0.1979 | -51.1281 | 94.4591 | 63.3215 | 9 | 0.3448 | 0.1043 | -0.067 | 0.1216 | -0.1663 | 0.4404 | 0.0767 | -0.304 | -0.0845 | 0.4204 | -0.0907 | -0.0592 | -0.3125 | 0.3313 | -0.0031 | 0.4482 | -0.0149 | 0.1047 | 0.2562 | -0.0275 | 0.1469 | -46.9801 | 105.6246 | 77.6261 | 10 | 0.4143 | 0.1719 | -0.1847 | 0.9245 | -0.662 | 1.8669 | 0.0719 | -0.1924 | 0.0871 | 0.7182 | -0.2988 | -0.1828 | -1.4685 | 0.6995 | -0.4221 | 0.6434 | -0.0997 | 0.0955 | 0.1026 | -0.1209 | 0.1405 | -44.7932 | 113.2793 | 71.5893 |
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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 1 through 64 )A1 - 64 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 65 through 176 )A65 - 176 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 177 through 199 )A177 - 199 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 200 through 237 )A200 - 237 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 238 through 297 )A238 - 297 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 298 through 320 )A298 - 320 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 1 through 40 )B1 - 40 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 41 through 184 )B41 - 184 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 185 through 221 )B185 - 221 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 222 through 318 )B222 - 318 | | | | | | | | | | | | | | | | | | | | |
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