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 | HKL-3000 | | 位相決定 | REFMAC | 5.5.0109精密化 | HKL-3000 | | データ削減 | HKL-3000 | | 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: 1.34→39.91 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.932 / SU ML: 0.037 / Isotropic thermal model: ISOTROPIC / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.062 / 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 | 0.19816 | 2476 | 5.1 % | RANDOM |
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Rwork | 0.16761 | - | - | - |
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obs | 0.1691 | 46411 | 97.3 % | - |
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all | - | 46411 | - | - |
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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: 9.423 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.13 Å2 | 0 Å2 | -0.53 Å2 |
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2- | - | -0.08 Å2 | 0 Å2 |
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3- | - | - | 0.09 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.059 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.34→39.91 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1952 | 0 | 2 | 312 | 2266 |
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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_d0.017 | 0.022 | 2151 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 1448 | X-RAY DIFFRACTION | r_angle_refined_deg1.648 | 1.983 | 2942 | X-RAY DIFFRACTION | r_angle_other_deg0.929 | 3 | 3541 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.127 | 5 | 291 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.3 | 23.478 | 92 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.351 | 15 | 364 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg10.495 | 15 | 19 | X-RAY DIFFRACTION | r_chiral_restr0.096 | 0.2 | 330 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.021 | 2515 | X-RAY DIFFRACTION | r_gen_planes_other0.002 | 0.02 | 442 | 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_it0.973 | 1.5 | 1382 | X-RAY DIFFRACTION | r_mcbond_other0.291 | 1.5 | 559 | X-RAY DIFFRACTION | r_mcangle_it1.741 | 2 | 2230 | X-RAY DIFFRACTION | r_scbond_it2.838 | 3 | 769 | X-RAY DIFFRACTION | r_scangle_it4.549 | 4.5 | 712 | 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: 1.342→1.376 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.246 | 180 | - |
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Rwork | 0.221 | 3166 | - |
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obs | - | - | 90.51 % |
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精密化 TLS | 手法: refined / Origin x: 24.4582 Å / Origin y: 4.3132 Å / Origin z: 15.9307 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0053 Å2 | 0.0062 Å2 | 0.0002 Å2 | - | 0.012 Å2 | 0.0026 Å2 | - | - | 0.0048 Å2 |
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L | 0.3735 °2 | 0.1123 °2 | 0.0472 °2 | - | 0.4731 °2 | 0.0953 °2 | - | - | 0.3677 °2 |
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S | -0.0079 Å ° | -0.0151 Å ° | 0.0178 Å ° | -0.0279 Å ° | 0.0052 Å ° | 0.0244 Å ° | -0.0067 Å ° | -0.0007 Å ° | 0.0026 Å ° |
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