ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0005精密化 | HKL-2000 | | データ削減 | DENZO | | データ削減 | HKL-2000 | | データスケーリング | SCALEPACK | | データスケーリング | PHASER | | 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: PDB ENTRY 2GTY 解像度: 1.79→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.643 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.117 / 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 | 0.1887 | 1108 | 5.1 % | RANDOM |
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Rwork | 0.1507 | - | - | - |
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all | 0.1507 | 21739 | - | - |
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obs | 0.1507 | 21726 | 94.14 % | - |
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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: 17.984 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.98 Å2 | 0 Å2 | -0.19 Å2 |
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2- | - | 0.88 Å2 | 0 Å2 |
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3- | - | - | 0.1 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.79→30 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1798 | 0 | 93 | 339 | 2230 |
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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_d0.019 | 0.021 | 2027 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.762 | 2 | 2766 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.244 | 5 | 273 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg42.765 | 23.571 | 84 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.063 | 15 | 292 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.734 | 15 | 10 | X-RAY DIFFRACTION | r_chiral_restr0.138 | 0.2 | 310 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 1538 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.187 | 0.2 | 874 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.308 | 0.2 | 1405 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.153 | 0.2 | 269 | 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_refined0.192 | 0.2 | 42 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.24 | 0.2 | 39 | 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_it1.099 | 1.5 | 1286 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.525 | 2 | 1996 | X-RAY DIFFRACTION | r_scbond_it2.885 | 3 | 843 | X-RAY DIFFRACTION | r_scangle_it3.817 | 4.5 | 759 | 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: 1.786→1.832 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.23 | 62 | - |
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Rwork | 0.203 | 1330 | - |
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obs | - | - | 79.4 % |
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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 | 0.3945 | -0.0363 | -0.1345 | 0.1649 | 0.1774 | 0.6073 | -0.0107 | -0.048 | -0.0052 | 0.0324 | 0.014 | -0.0199 | 0.0097 | -0.0095 | -0.0033 | -0.0172 | -0.0018 | 0.0066 | -0.0126 | 0.0107 | -0.0152 | 15.3361 | 30.3698 | 11.3519 | 2 | 0.19 | -0.1082 | 0.0033 | 0.1601 | 0.0302 | 1.017 | -0.0056 | 0.0275 | -0.0054 | -0.0141 | -0.0183 | -0.0102 | -0.006 | -0.001 | 0.0239 | -0.0091 | -0.0025 | 0.0023 | -0.0157 | 0.0124 | -0.0221 | 11.5825 | 22.2438 | -6.4988 |
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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 | AA0 - 121 | 1 - 121 | 2 | X-RAY DIFFRACTION | 2 | BB0 - 121 | 1 - 121 | | | | |
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