ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | MOLREP | | 位相決定 | | REFMAC | 5.5.0066精密化 | | PDB_EXTRACT | 3.005 | データ抽出 | | HKL-2000 | | データ収集 | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB entry 3IEY 解像度: 2.2→41.38 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.168 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.199 / 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 | 0.27712 | 643 | 5 % | RANDOM |
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Rwork | 0.24827 | - | - | - |
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obs | 0.24964 | 12345 | 99.84 % | - |
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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: 35.247 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.39 Å2 | 0.2 Å2 | 0 Å2 |
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2- | - | 0.39 Å2 | 0 Å2 |
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3- | - | - | -0.59 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.2→41.38 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1269 | 0 | 0 | 0 | 1269 |
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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_d0.01 | 0.022 | 1301 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.266 | 1.982 | 1752 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.836 | 5 | 148 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.093 | 23.226 | 62 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg18.388 | 15 | 251 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.382 | 15 | 9 | X-RAY DIFFRACTION | r_chiral_restr0.103 | 0.2 | 184 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.021 | 968 | 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_it0.646 | 1.5 | 740 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.206 | 2 | 1203 | X-RAY DIFFRACTION | r_scbond_it1.747 | 3 | 561 | X-RAY DIFFRACTION | r_scangle_it2.853 | 4.5 | 549 | 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: 2.2→2.257 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.378 | 50 | - |
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Rwork | 0.277 | 907 | - |
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obs | - | - | 99.9 % |
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精密化 TLS | 手法: refined / Origin x: 27.6367 Å / Origin y: -21.9329 Å / Origin z: 6.3322 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0885 Å2 | -0.0305 Å2 | -0.0306 Å2 | - | 0.0878 Å2 | 0.0143 Å2 | - | - | 0.048 Å2 |
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L | 2.2978 °2 | 0.2771 °2 | 1.1937 °2 | - | 1.2946 °2 | 0.606 °2 | - | - | 1.3721 °2 |
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S | -0.0712 Å ° | -0.0781 Å ° | 0.2102 Å ° | 0.0363 Å ° | -0.0753 Å ° | -0.0626 Å ° | -0.0489 Å ° | -0.021 Å ° | 0.1465 Å ° |
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