ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | HKL-3000 | | 位相決定 | SHELXD | | 位相決定 | SHELXE | | モデル構築 | MLPHARE | | 位相決定 | 直接法 | | モデル構築 | RESOLVE | | モデル構築 | Coot | | モデル構築 | ARP/wARP | | モデル構築 | REFMAC | 5.5.0102精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | 直接法 | | 位相決定 | RESOLVE | | 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: 1.9→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.731 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.143 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.21658 | 2188 | 5.1 % | RANDOM |
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Rwork | 0.17702 | - | - | - |
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all | 0.17907 | 43299 | - | - |
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obs | 0.17907 | 43299 | 99.79 % | - |
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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: MASK |
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原子変位パラメータ | Biso mean: 18.625 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.3 Å2 | 0 Å2 | -1.03 Å2 |
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2- | - | 0.27 Å2 | 0 Å2 |
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3- | - | - | -0.96 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4213 | 0 | 2 | 518 | 4733 |
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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_d0.015 | 0.022 | 4343 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.37 | 1.968 | 5883 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.182 | 5 | 530 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg39.342 | 22.311 | 212 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.851 | 15 | 768 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.885 | 15 | 57 | X-RAY DIFFRACTION | r_chiral_restr0.094 | 0.2 | 664 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.021 | 3283 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | 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_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | 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_it0.902 | 1.5 | 2646 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.772 | 2 | 4280 | X-RAY DIFFRACTION | r_scbond_it2.929 | 3 | 1697 | X-RAY DIFFRACTION | r_scangle_it5.1 | 4.5 | 1603 | 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: 1.896→1.946 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.31 | 170 | - |
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Rwork | 0.198 | 2880 | - |
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obs | - | 3050 | 99.06 % |
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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 | 0.2017 | 0.0493 | -0.2526 | 0.6585 | 0.4948 | 2.3909 | -0.0026 | -0.0091 | 0.0049 | -0.0524 | -0.0228 | 0.0343 | 0.0385 | -0.16 | 0.0254 | 0.0259 | 0.0053 | -0.0016 | 0.0317 | -0.0066 | 0.0533 | 24.6003 | -0.5884 | 0.8198 | 2 | 0.4348 | -0.0628 | 0.6616 | 0.6217 | -0.3381 | 3.3612 | -0.0368 | -0.0288 | 0.004 | -0.0433 | -0.0119 | -0.0347 | -0.0438 | 0.2174 | 0.0486 | 0.009 | -0.0016 | -0.0047 | 0.0421 | 0.014 | 0.0495 | 49.0023 | -2.2229 | -0.1053 | 3 | 2.4252 | 0.3643 | 0.1339 | 1.1249 | -0.0149 | 1.4726 | -0.0049 | -0.0887 | 0.0548 | 0.1032 | 0.0651 | 0.0371 | -0.0381 | 0.012 | -0.0603 | 0.0686 | 0.004 | -0.0016 | 0.0096 | 0.0002 | 0.0076 | 24.6394 | 13.8946 | 57.8642 | 4 | 2.1593 | -0.0822 | -0.1212 | 1.1783 | -0.2305 | 1.4589 | 0.0098 | 0.0514 | -0.0617 | -0.0072 | 0.0462 | 0.0066 | 0.0319 | 0.0053 | -0.056 | 0.0415 | -0.0062 | -0.0185 | 0.0056 | 0.003 | 0.0159 | 23.0141 | 11.8196 | 32.2255 |
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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 | A1 - 141 | 2 | X-RAY DIFFRACTION | 2 | B5 - 140 | 3 | X-RAY DIFFRACTION | 3 | C5 - 139 | 4 | X-RAY DIFFRACTION | 4 | D5 - 142 | | | | |
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