ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0189精密化 | Coot | 0.8.9モデル構築 | XDS | 1.02 | データ削減 | XDS | 1.02 | データスケーリング | PHASER | 7.0.047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: 6scb 解像度: 1.5→47.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.487 / SU ML: 0.03 / 交差検証法: FREE R-VALUE / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.013 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.185 | 2621 | 5.2 % | RANDOM |
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Rwork | 0.1736 | - | - | - |
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obs | 0.1743 | 47701 | 99.85 % | - |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso max: 47.14 Å2 / Biso mean: 29.19 Å2 / Biso min: 21.93 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 21.44 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 21.44 Å2 | 0 Å2 |
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3- | - | - | -42.89 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.5→47.64 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2119 | 0 | 18 | 162 | 2299 |
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Biso mean | - | - | 33.23 | 36.68 | - |
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残基数 | - | - | - | - | 270 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.009 | 0.019 | 2294 | X-RAY DIFFRACTION | r_angle_refined_deg1.233 | 1.942 | 3125 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg4.55 | 5 | 292 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.014 | 24.955 | 111 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.103 | 15 | 365 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg11.449 | 15 | 7 | X-RAY DIFFRACTION | r_chiral_restr0.094 | 0.2 | 340 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 1818 | | | | | | | | |
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Refine LS restraints NCS | Ens-ID: 1 / 数: 8674 / Refine-ID: X-RAY DIFFRACTION / タイプ: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05 |
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LS精密化 シェル | 解像度: 1.5→1.54 Å / Rfactor Rfree error: 0
| Rfactor | 反射数 | %反射 |
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Rfree | 0.305 | 174 | - |
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Rwork | 0.258 | 3453 | - |
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obs | - | - | 98.83 % |
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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 | 8.4675 | 1.5081 | -0.9895 | 0.769 | -0.9251 | 2.9113 | -0.053 | -0.1078 | 0.0024 | -0.0045 | 0.0208 | -0.1737 | 0.0723 | 0.3001 | 0.0322 | 0.1654 | 0.0384 | 0.006 | 0.1705 | 0.0038 | 0.3534 | 7.7159 | -40.8094 | 24.8334 | 2 | 3.9024 | -2.4255 | 3.8808 | 6.3234 | -0.3646 | 4.7332 | 0.2626 | -0.1931 | -0.2638 | -0.0596 | -0.0277 | 0.2024 | 0.3296 | -0.2497 | -0.2348 | 0.18 | -0.0123 | 0.0244 | 0.1227 | 0.007 | 0.3188 | -2.6349 | -41.3823 | 20.6619 | 3 | 3.0529 | -2.5072 | -0.15 | 5.2621 | 2.8923 | 2.5033 | 0.1807 | 0.1632 | -0.0984 | -0.1799 | -0.1894 | 0.1507 | 0.0001 | -0.1911 | 0.0087 | 0.0273 | -0.0434 | 0.0012 | 0.1968 | 0.0235 | 0.2737 | -10.0722 | -29.4594 | 18.9525 | 4 | 2.219 | 0.5679 | -0.9287 | 0.2072 | -0.6453 | 3.1311 | -0.0384 | 0.0174 | -0.0258 | -0.043 | 0.0018 | 0.003 | 0.2432 | -0.0278 | 0.0366 | 0.0198 | -0.0031 | 0.0108 | 0.0637 | 0.0116 | 0.2739 | 0.7339 | -29.7028 | 20.0902 | 5 | 4.1201 | 0.5664 | 1.8589 | 4.8621 | 1.5135 | 6.1859 | -0.0543 | -0.0856 | 0.2403 | 0.4363 | 0.1351 | 0.1071 | -0.2808 | -0.3169 | -0.0808 | 0.071 | 0.0511 | 0.0214 | 0.1407 | 0.0116 | 0.2668 | -3.4961 | -17.3356 | 17.4227 | 6 | 3.1802 | -0.7681 | 2.6496 | 13.3972 | -1.4615 | 2.2624 | -0.1796 | -0.1134 | 0.1531 | 0.1492 | 0.0606 | -0.2341 | -0.1707 | -0.1022 | 0.119 | 0.0903 | 0.0214 | 0.0178 | 0.1472 | 0.0042 | 0.2432 | 2.3527 | -14.6087 | 14.8376 | 7 | 1.815 | -0.5437 | 0.5307 | 1.1836 | -1.3122 | 3.4094 | -0.0423 | -0.0233 | 0.0713 | -0.057 | 0.0672 | -0.0411 | -0.0702 | 0.052 | -0.0249 | 0.0163 | -0.0101 | -0.0113 | 0.0744 | 0.0027 | 0.2797 | 4.509 | -19.4767 | 7.1155 | 8 | 2.2498 | -1.6882 | -0.8212 | 5.8712 | 2.8746 | 4.8011 | 0.0387 | 0.2024 | 0.1264 | -0.2651 | -0.0046 | -0.1985 | -0.3138 | 0.1437 | -0.0341 | 0.0235 | -0.0052 | 0.0031 | 0.0947 | 0.024 | 0.2825 | 6.1639 | -17.5975 | -2.2126 | 9 | 0.6206 | -0.4874 | -0.0955 | 8.1784 | 0.7778 | 1.8641 | -0.0158 | 0.0696 | 0.1026 | -0.2739 | 0.0428 | 0.1212 | -0.0761 | -0.1297 | -0.027 | 0.0641 | 0.0155 | -0.0346 | 0.1521 | 0.0038 | 0.2676 | -1.9926 | -18.5219 | -4.3266 | 10 | 5.0145 | 1.2685 | 0.7927 | 2.0911 | -1.0185 | 1.7303 | -0.0249 | -0.3613 | -0.0943 | 0.1752 | 0.0654 | 0.1713 | -0.2707 | 0.0425 | -0.0405 | 0.0467 | -0.014 | -0.0193 | 0.1491 | 0.0027 | 0.2769 | 10.7158 | -23.6187 | 22.4731 | 11 | 6.1717 | 3.2063 | -2.8323 | 2.5525 | -1.8565 | 4.0223 | -0.1063 | 0.2026 | 0.1468 | -0.1392 | 0.0005 | 0.0719 | -0.0961 | -0.2805 | 0.1057 | 0.2155 | 0.064 | -0.0019 | 0.1624 | -0.0004 | 0.362 | 15.427 | -9.4137 | 24.7699 | 12 | 4.2114 | -2.0008 | 0.8631 | 4.2623 | -0.5873 | 2.099 | -0.0015 | 0.1052 | 0.2705 | -0.1349 | 0.0245 | -0.1274 | -0.2546 | 0.274 | -0.023 | 0.0732 | -0.0382 | 0.0058 | 0.1229 | 0.0215 | 0.2653 | 32.589 | -14.6151 | 17.0469 | 13 | 4.6877 | -0.2488 | 1.4273 | 0.4654 | -0.0684 | 3.6175 | 0.0464 | -0.0399 | -0.0347 | -0.0536 | -0.018 | 0.034 | -0.1176 | 0.0345 | -0.0284 | 0.0211 | -0.029 | -0.0184 | 0.0951 | 0.0144 | 0.246 | 24.2581 | -19.573 | 19.8354 | 14 | 2.2038 | 0.0926 | 0.4589 | 3.1125 | 1.2681 | 3.4911 | -0.0446 | -0.0057 | -0.0512 | 0.0714 | 0.0579 | -0.1293 | -0.0273 | 0.2034 | -0.0132 | 0.0042 | 0.0047 | 0.0072 | 0.0962 | 0.008 | 0.2724 | 22.8073 | -25.7255 | 10.4576 | 15 | 3.7293 | 0.2917 | -4.9719 | 4.6452 | -3.6333 | 8.9264 | 0.472 | 0.1973 | 0.4119 | 0.0995 | -0.0075 | -0.0267 | -0.7237 | -0.2543 | -0.4645 | 0.1837 | 0.0145 | -0.0199 | 0.1469 | -0.0054 | 0.3141 | 16.279 | -16.9647 | 2.3075 | 16 | 1.1864 | 0.0002 | 1.0201 | 4.2713 | -1.1876 | 3.602 | 0.0203 | 0.054 | -0.1881 | 0.0465 | 0.0378 | 0.0481 | 0.346 | 0.1063 | -0.0581 | 0.0686 | -0.003 | 0.0248 | 0.0806 | -0.0142 | 0.3101 | 21.2872 | -31.8942 | 0.6393 | 17 | 1.9506 | -2.2129 | 0.6728 | 5.4482 | -1.9906 | 5.2639 | 0.1569 | 0.2032 | -0.154 | -0.2631 | -0.1308 | 0.293 | 0.4449 | -0.1714 | -0.0261 | 0.0602 | -0.0318 | -0.0099 | 0.1236 | -0.0234 | 0.3062 | 17.3467 | -26.8408 | -7.3703 | 18 | 2.091 | -0.2054 | 0.7437 | 5.5686 | -1.2311 | 4.4445 | -0.0702 | 0.0157 | -0.1821 | -0.1045 | 0.127 | -0.0641 | 0.2479 | 0.1349 | -0.0568 | 0.0716 | 0.0117 | 0.0258 | 0.1268 | -0.0024 | 0.2948 | 25.6865 | -27.21 | -9.1636 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A24 - 32 | 2 | X-RAY DIFFRACTION | 2 | A33 - 39 | 3 | X-RAY DIFFRACTION | 3 | A40 - 53 | 4 | X-RAY DIFFRACTION | 4 | A54 - 78 | 5 | X-RAY DIFFRACTION | 5 | A79 - 85 | 6 | X-RAY DIFFRACTION | 6 | A86 - 89 | 7 | X-RAY DIFFRACTION | 7 | A90 - 121 | 8 | X-RAY DIFFRACTION | 8 | A122 - 134 | 9 | X-RAY DIFFRACTION | 9 | A135 - 151 | 10 | X-RAY DIFFRACTION | 10 | B9 - 21 | 11 | X-RAY DIFFRACTION | 11 | B22 - 33 | 12 | X-RAY DIFFRACTION | 12 | B34 - 51 | 13 | X-RAY DIFFRACTION | 13 | B52 - 68 | 14 | X-RAY DIFFRACTION | 14 | B69 - 98 | 15 | X-RAY DIFFRACTION | 15 | B99 - 103 | 16 | X-RAY DIFFRACTION | 16 | B104 - 124 | 17 | X-RAY DIFFRACTION | 17 | B125 - 134 | 18 | X-RAY DIFFRACTION | 18 | B135 - 150 | | | | | | | | | | | | | | | | | | |
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