ソフトウェア | 名称 | バージョン | 分類 |
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Blu-Ice | Maxデータ収集 | CRANK | | 位相決定 | REFMAC | 5.5.0102精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.4→29.55 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.649 / SU ML: 0.137 / Isotropic thermal model: Refined Individually / 交差検証法: THROUGHOUT / ESU R: 0.544 / ESU R Free: 0.277 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.24498 | 1677 | 5.1 % | RANDOM |
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Rwork | 0.1886 | - | - | - |
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all | 0.19147 | 31524 | - | - |
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obs | 0.19147 | 31524 | 98.58 % | - |
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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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 49.679 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -3.09 Å2 | 0 Å2 | 0.99 Å2 |
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2- | - | 0.52 Å2 | 0 Å2 |
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3- | - | - | 2.62 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.4→29.55 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6337 | 0 | 30 | 183 | 6550 |
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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_d0.008 | 0.021 | 6705 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 4602 | X-RAY DIFFRACTION | r_angle_refined_deg1.282 | 1.925 | 9180 | X-RAY DIFFRACTION | r_angle_other_deg0.791 | 3 | 11056 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg1.906 | 5 | 816 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg23.35 | 22.667 | 330 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg8.779 | 15 | 1001 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg9.7 | 15 | 69 | X-RAY DIFFRACTION | r_chiral_restr0.074 | 0.2 | 945 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.021 | 7607 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1476 | X-RAY DIFFRACTION | r_mcbond_it0.732 | 1.5 | 4035 | X-RAY DIFFRACTION | r_mcbond_other0.17 | 1.5 | 1613 | X-RAY DIFFRACTION | r_mcangle_it1.317 | 2 | 6517 | X-RAY DIFFRACTION | r_scbond_it2.165 | 3 | 2670 | X-RAY DIFFRACTION | r_scangle_it3.355 | 4.5 | 2663 | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.4→2.462 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.3 | 114 | - |
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Rwork | 0.231 | 2299 | - |
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obs | - | 2299 | 97.85 % |
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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 | 2.1015 | -0.0247 | -0.3806 | 3.2307 | -0.3304 | 4.8843 | -0.104 | 0.4972 | 0.0588 | -0.5427 | 0.1567 | 0.5409 | -0.1218 | -0.3686 | -0.0527 | 0.1815 | -0.0752 | -0.1023 | 0.1986 | 0.0086 | 0.1219 | 8.3159 | 24.263 | 0.7538 | 2 | 4.9141 | -2.2687 | -1.5115 | 16.3857 | 5.2172 | 8.0939 | -0.1995 | 0.3553 | -0.066 | -0.5172 | 0.5925 | -0.7105 | 0.2932 | 0.7957 | -0.393 | 0.1684 | -0.1245 | -0.0239 | 0.3131 | -0.0165 | 0.0602 | 20.4185 | 19.3132 | -1.2127 | 3 | 5.184 | 3.3295 | 2.1147 | 2.8464 | 0.5469 | 2.1947 | -0.1584 | -0.068 | 0.2198 | 0.0413 | -0.048 | 0.157 | 0.0041 | -0.0479 | 0.2065 | 0.1984 | 0.0276 | 0.0312 | 0.0572 | -0.0612 | 0.1156 | 20.526 | 30.598 | 20.7458 | 4 | 1.9607 | 0.7092 | -0.4953 | 2.8516 | 0.4318 | 2.2889 | -0.0538 | -0.108 | -0.1491 | 0.1683 | -0.0336 | -0.1919 | 0.1591 | 0.33 | 0.0874 | 0.0231 | 0.0143 | -0.0055 | 0.0569 | 0.0256 | 0.0268 | 36.8917 | 24.8303 | 25.3313 | 5 | 0.1309 | 1.8018 | 0.5678 | 33.5707 | 10.47 | 3.2688 | -0.0642 | -0.0054 | -0.4271 | -0.9934 | 1.2032 | -3.4818 | -0.2605 | 0.3715 | -1.139 | 1.1276 | 0.2697 | 0.0289 | 0.6683 | 0.2686 | 2.0694 | 37.4189 | 3.8453 | 19.4158 | 6 | 1.9986 | 0.0494 | 0.2915 | 4.0827 | 0.71 | 4.8157 | 0.0321 | -0.0286 | -0.3811 | 0.0929 | -0.218 | -0.0332 | 0.4779 | 0.1377 | 0.1858 | 0.1171 | -0.0119 | 0.0553 | 0.0273 | 0.003 | 0.1064 | 24.7543 | 13.1275 | 25.4285 | 7 | 5.6543 | 0.6087 | 1.4432 | 4.1028 | 0.7845 | 4.154 | -0.0397 | 1.4958 | 0.2516 | -0.7109 | 0.1265 | -0.516 | 0.0798 | 0.4706 | -0.0869 | 0.1425 | 0.0289 | 0.1135 | 0.5019 | 0.1569 | 0.1592 | 69.0601 | 60.5091 | 4.2434 | 8 | 9.0057 | -3.549 | 3.3123 | 14.8313 | -0.8296 | 6.9231 | -0.0279 | 0.8093 | 0.3308 | -1.0314 | 0.023 | 0.6971 | -0.5045 | -0.3714 | 0.0049 | 0.3021 | -0.0308 | 0.0082 | 0.598 | 0.1219 | 0.1002 | 57.01 | 65.8202 | 1.7698 | 9 | 5.8012 | 1.946 | -1.5876 | 2.5188 | -0.5693 | 1.5049 | 0.078 | 0.0941 | -0.3467 | 0.0462 | -0.0792 | -0.2703 | 0.1492 | 0.1134 | 0.0012 | 0.0813 | 0.0307 | -0.0186 | 0.1052 | 0.0749 | 0.1311 | 56.7337 | 51.3479 | 22.2607 | 10 | 2.5861 | 0.5221 | 0.0333 | 3.0067 | -0.1899 | 1.9901 | 0.112 | -0.2548 | 0.1741 | 0.1907 | 0.0134 | 0.2052 | 0.0693 | -0.2764 | -0.1254 | 0.0179 | -0.0194 | 0.0122 | 0.0757 | 0.0072 | 0.0303 | 40.23 | 56.4325 | 28.2286 | 11 | 5.1226 | -2.0024 | 0.4506 | 9.1822 | -3.6513 | 3.6803 | 0.1349 | 0.0829 | 0.8246 | 0.2617 | 0.0017 | 0.2809 | -0.5588 | -0.2383 | -0.1367 | 0.1556 | 0.0335 | 0.025 | 0.0833 | -0.0607 | 0.2888 | 42.1452 | 75.7584 | 28.3628 | 12 | 2.3997 | 0.8104 | -1.0082 | 3.2763 | -1.7976 | 2.4538 | 0.2262 | -0.4212 | 0.4736 | 0.669 | -0.3238 | -0.2139 | -0.5583 | 0.3443 | 0.0976 | 0.2193 | -0.0544 | -0.0596 | 0.1705 | -0.0223 | 0.2066 | 53.2039 | 67.7331 | 29.5393 |
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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 | A7 - 102 | 2 | X-RAY DIFFRACTION | 2 | A103 - 137 | 3 | X-RAY DIFFRACTION | 3 | A138 - 173 | 4 | X-RAY DIFFRACTION | 4 | A174 - 317 | 5 | X-RAY DIFFRACTION | 5 | A318 - 339 | 6 | X-RAY DIFFRACTION | 6 | A340 - 403 | 7 | X-RAY DIFFRACTION | 7 | B9 - 101 | 8 | X-RAY DIFFRACTION | 8 | B102 - 136 | 9 | X-RAY DIFFRACTION | 9 | B137 - 173 | 10 | X-RAY DIFFRACTION | 10 | B174 - 317 | 11 | X-RAY DIFFRACTION | 11 | B318 - 345 | 12 | X-RAY DIFFRACTION | 12 | B346 - 403 | | | | | | | | | | | | |
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