ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.3.0036精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | SHARP | | 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→46.27 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.499 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.116 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.196 | 1195 | 2.2 % | RANDOM |
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Rwork | 0.172 | - | - | - |
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obs | 0.173 | 51167 | 100 % | - |
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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: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 29.33 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.45 Å2 | -0.72 Å2 | 0 Å2 |
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2- | - | -1.45 Å2 | 0 Å2 |
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3- | - | - | 2.17 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.95→46.27 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4601 | 0 | 8 | 333 | 4942 |
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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 | 0.021 | 4751 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.227 | 1.935 | 6389 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.483 | 5 | 614 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.279 | 25.333 | 225 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.963 | 15 | 687 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.478 | 15 | 14 | X-RAY DIFFRACTION | r_chiral_restr0.06 | 0.2 | 697 | X-RAY DIFFRACTION | r_gen_planes_refined0.002 | 0.02 | 3694 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.215 | 0.2 | 2055 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.318 | 0.2 | 3209 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.163 | 0.2 | 385 | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined0.127 | 0.2 | 35 | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.245 | 0.2 | 46 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.148 | 0.2 | 5 | 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_it1.842 | 1.5 | 3122 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it2.558 | 2 | 4759 | X-RAY DIFFRACTION | r_scbond_it4.368 | 3 | 1854 | X-RAY DIFFRACTION | r_scangle_it5.933 | 4.5 | 1630 | 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 | 0.292 | 72 | - |
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Rwork | 0.291 | 3081 | - |
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obs | - | - | 100 % |
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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 | 1.4055 | -0.1628 | -0.7619 | 3.1187 | -0.1673 | 1.2502 | -0.0692 | -0.1537 | -0.303 | 0.5982 | 0.0104 | 0.5898 | 0.1134 | 0.105 | 0.0588 | -0.0067 | -0.0282 | 0.141 | -0.0816 | 0.0078 | 0.0477 | 28.3377 | -2.5135 | 23.8956 | 2 | 0.9499 | -0.2055 | -0.0105 | 3.2415 | 0.5538 | 0.5398 | -0.0709 | -0.0129 | -0.1745 | 0.0504 | -0.0443 | 0.3547 | -0.078 | 0.0119 | 0.1152 | -0.0875 | -0.0225 | 0.0787 | -0.1062 | -0.0165 | -0.1153 | 27.5487 | 24.618 | 17.1063 | 3 | 3.9273 | -0.3396 | -1.9964 | 2.6051 | 0.8118 | 3.5804 | 0.0153 | -0.2262 | 0.293 | 0.3345 | -0.0229 | 0.1 | -0.1734 | -0.0103 | 0.0075 | 0.076 | -0.0013 | 0.0188 | -0.0469 | -0.0532 | -0.1739 | 25.34 | 44.8144 | 36.3818 |
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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 - 249 | 2 | X-RAY DIFFRACTION | 2 | A250 - 461 | 3 | X-RAY DIFFRACTION | 3 | A462 - 613 | | | |
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