ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0019精密化 | SBC-Collect | | データ収集 | 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: 単波長異常分散 / 解像度: 1.95→41.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.016 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.134 / 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 | 0.21435 | 2376 | 5.1 % | RANDOM |
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Rwork | 0.18564 | - | - | - |
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obs | 0.18713 | 44665 | 99.26 % | - |
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all | - | 44665 | - | - |
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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 mean: 31.538 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.5 Å2 | 0.25 Å2 | 0 Å2 |
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2- | - | 0.5 Å2 | 0 Å2 |
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3- | - | - | -0.76 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.95→41.24 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3798 | 0 | 52 | 403 | 4253 |
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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_d0.012 | 0.022 | 4149 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.24 | 1.976 | 5700 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.524 | 5 | 529 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.847 | 24.354 | 209 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.577 | 15 | 654 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg12.196 | 15 | 30 | X-RAY DIFFRACTION | r_chiral_restr0.093 | 0.2 | 611 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 3299 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.193 | 0.2 | 1936 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.302 | 0.2 | 2753 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.15 | 0.2 | 360 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.246 | 0.2 | 53 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.239 | 0.2 | 24 | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it0.895 | 1.5 | 2598 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.045 | 2 | 4075 | X-RAY DIFFRACTION | r_scbond_it2.013 | 3 | 1808 | X-RAY DIFFRACTION | r_scangle_it2.79 | 4.5 | 1601 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.95→2 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.308 | 170 | - |
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Rwork | 0.263 | 3015 | - |
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obs | - | - | 91.44 % |
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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 | 27.2644 | -14.7536 | -5.5991 | 10.6489 | 3.928 | 6.5438 | 0.0272 | 0.4374 | 0.5478 | -0.2958 | -0.2854 | -0.4717 | -0.791 | -0.2994 | 0.2582 | -0.0546 | 0.0303 | -0.0921 | -0.0532 | -0.0063 | -0.1046 | -30.557 | 57.687 | 15.301 | 2 | 5.2065 | 3.0549 | 0.663 | 3.9095 | 0.9982 | 2.4969 | 0.04 | 0.2844 | 0.4182 | 0.0513 | -0.0611 | 0.2059 | -0.2023 | -0.0482 | 0.0211 | -0.078 | 0.0136 | 0.0091 | -0.0215 | 0.0489 | -0.0431 | -13.854 | 53.488 | 19.545 | 3 | 3.5112 | -0.7447 | -1.6654 | 5.259 | -1.1194 | 3.947 | 0.0416 | 0.6418 | 0.1283 | -0.4845 | -0.2314 | -0.2827 | -0.0083 | -0.2645 | 0.1898 | -0.0873 | 0.0299 | 0.0673 | 0.0287 | 0.0963 | -0.1043 | -5.409 | 53.361 | 6.973 | 4 | 1.71 | -0.0614 | -0.1374 | 0.8409 | -0.7628 | 1.8847 | -0.0027 | 0.1236 | 0.0756 | 0.0359 | -0.1561 | -0.2756 | 0.0507 | 0.1307 | 0.1588 | -0.1024 | 0.0041 | -0.007 | 0.0124 | 0.0507 | 0.0253 | -0.67 | 46.864 | 22.645 | 5 | 1.4084 | 0.7587 | 1.4714 | 4.374 | 1.3732 | 4.063 | 0.1118 | 0.2668 | -0.1409 | -0.1559 | 0.0558 | -0.5977 | 0.3944 | 0.4397 | -0.1676 | 0.02 | 0.0418 | 0.0091 | -0.0023 | -0.0193 | -0.0265 | -18.376 | 24.146 | 11.545 | 6 | 4.7164 | 3.0952 | 1.8809 | 2.2884 | 1.484 | 1.109 | -0.0563 | 0.0737 | 0.0473 | -0.0937 | -0.0901 | 0.2687 | 0.0092 | -0.0096 | 0.1465 | 0.021 | -0.0212 | -0.0308 | 0.0724 | -0.0471 | 0.0287 | -26.423 | 37.219 | 19.585 | 7 | 6.8274 | -4.7161 | 4.8114 | 4.9646 | -2.2313 | 5.6162 | -0.008 | 0.0338 | 0.5674 | -0.1159 | -0.0859 | -0.2806 | -0.316 | 0.0143 | 0.0939 | -0.0754 | -0.0405 | -0.0095 | -0.0528 | -0.0496 | -0.0521 | -22.689 | 56.242 | 28.547 | 8 | 2.741 | -0.1342 | -0.8822 | 4.6552 | 0.9399 | 5.2358 | -0.1111 | -0.3156 | 0.2741 | 0.382 | -0.15 | -0.0424 | -0.5414 | -0.1794 | 0.2611 | -0.0323 | 0.0223 | -0.0898 | -0.0618 | -0.1326 | -0.0897 | -31.077 | 64.215 | 38.103 | 9 | 1.4802 | -0.2088 | -0.1003 | 2.746 | 1.3698 | 1.596 | -0.0273 | -0.1599 | 0.0212 | 0.0506 | -0.2861 | 0.4265 | 0.0233 | -0.3696 | 0.3134 | -0.1016 | -0.0137 | -0.0166 | 0.0731 | -0.1039 | -0.0332 | -35.882 | 49.313 | 30.085 | 10 | 0.7949 | 0.3677 | -1.0586 | 1.462 | -0.0374 | 5.9093 | -0.1547 | -0.23 | -0.0224 | 0.0101 | 0.0203 | 0.2137 | 0.1023 | -0.2763 | 0.1345 | -0.0406 | 0.0062 | 0.0345 | 0.0303 | 0.0034 | -0.0788 | -18.331 | 39.7 | 52.983 | 11 | 7.613 | -0.5321 | 4.3725 | 0.093 | -0.1429 | 2.9861 | -0.2516 | -0.1527 | 0.0793 | -0.0332 | 0.0448 | -0.0833 | -0.0474 | 0.0622 | 0.2067 | 0.0028 | -0.0211 | -0.0339 | 0.0786 | -0.004 | -0.0393 | -9.818 | 44.18 | 38.627 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA5 - 14 | 8 - 17 | 2 | X-RAY DIFFRACTION | 2 | AA15 - 29 | 18 - 32 | 3 | X-RAY DIFFRACTION | 3 | AA30 - 84 | 33 - 87 | 4 | X-RAY DIFFRACTION | 4 | AA85 - 129 | 88 - 132 | 5 | X-RAY DIFFRACTION | 4 | AA164 - 185 | 167 - 188 | 6 | X-RAY DIFFRACTION | 4 | AA250 - 256 | 253 - 259 | 7 | X-RAY DIFFRACTION | 5 | AA130 - 163 | 133 - 166 | 8 | X-RAY DIFFRACTION | 5 | AA194 - 234 | 197 - 237 | 9 | X-RAY DIFFRACTION | 6 | AA186 - 193 | 189 - 196 | 10 | X-RAY DIFFRACTION | 6 | AA235 - 249 | 238 - 252 | 11 | X-RAY DIFFRACTION | 7 | BB15 - 29 | 18 - 32 | 12 | X-RAY DIFFRACTION | 8 | BB30 - 84 | 33 - 87 | 13 | X-RAY DIFFRACTION | 9 | BB85 - 129 | 88 - 132 | 14 | X-RAY DIFFRACTION | 9 | BB164 - 185 | 167 - 188 | 15 | X-RAY DIFFRACTION | 9 | BB250 - 256 | 253 - 259 | 16 | X-RAY DIFFRACTION | 10 | BB130 - 163 | 133 - 166 | 17 | X-RAY DIFFRACTION | 10 | BB194 - 234 | 197 - 237 | 18 | X-RAY DIFFRACTION | 11 | BB186 - 193 | 189 - 196 | 19 | X-RAY DIFFRACTION | 11 | BB235 - 249 | 238 - 252 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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