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 | PHENIX | | モデル構築 | 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 | PHENIX | | 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: 2.09→35.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 18.794 / SU ML: 0.227 / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.33 / ESU R Free: 0.255 / 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 | 0.30189 | 1625 | 5 % | RANDOM |
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Rwork | 0.24174 | - | - | - |
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all | 0.24486 | 30611 | - | - |
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obs | 0.24486 | 30611 | 96.34 % | - |
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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: 45.78 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.28 Å2 | 0 Å2 | -0.16 Å2 |
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2- | - | -0.22 Å2 | 0 Å2 |
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3- | - | - | -0.11 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.09→35.7 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4447 | 0 | 2 | 94 | 4543 |
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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_d0.016 | 0.022 | 4709 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.578 | 1.972 | 6430 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.09 | 5 | 617 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg42.847 | 26.31 | 252 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg20.147 | 15 | 866 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.07 | 15 | 25 | X-RAY DIFFRACTION | r_chiral_restr0.101 | 0.2 | 736 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.021 | 3641 | 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_it0.819 | 1.5 | 2909 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.532 | 2 | 4690 | X-RAY DIFFRACTION | r_scbond_it2.311 | 3 | 1800 | X-RAY DIFFRACTION | r_scangle_it3.882 | 4.5 | 1711 | 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: 2.094→2.148 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.383 | 73 | - |
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Rwork | 0.334 | 1357 | - |
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obs | - | 1430 | 57.94 % |
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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 | 0.2035 | -0.1787 | 0.1974 | 0.3793 | -0.1413 | 0.2054 | 0.0152 | 0.0649 | -0.028 | -0.0194 | 0.0083 | -0.0355 | 0.0088 | 0.0537 | -0.0235 | 0.057 | 0.0064 | 0.0312 | 0.1041 | -0.0006 | 0.0754 | 60.0572 | 2.5562 | 61.0833 | 2 | 0.6329 | 0.1763 | 0.495 | 0.0756 | 0.2017 | 0.5865 | -0.1171 | 0.2287 | 0.1389 | -0.0325 | 0.0165 | 0.0322 | -0.1225 | 0.1226 | 0.1005 | 0.223 | -0.022 | -0.0067 | 0.2324 | 0.032 | 0.2536 | 89.0042 | 1.1471 | 61.0516 |
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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 | A-10 - 9999 | 2 | X-RAY DIFFRACTION | 2 | B-10 - 9999 | | |
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