ソフトウェア | 名称 | バージョン | 分類 |
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BUSTER | 2.11.1精密化 | HKL | | データ削減 | SCALEPACK | | データスケーリング | MOLREP | | 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 2DU8 解像度: 2.75→27.65 Å / Cor.coef. Fo:Fc: 0.9322 / Cor.coef. Fo:Fc free: 0.8818 / 交差検証法: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.391 詳細: POOR DENSITY IS PRESENT FOR RESIDUES A25, A26, A27, A28, A297, A302, A335, A336, A337, A338, B25, B26, B27, B28, B29, B30, B56, B57, B58, B59, B99, B100, B101, B174, B175, B194,B195, B196, ...詳細: POOR DENSITY IS PRESENT FOR RESIDUES A25, A26, A27, A28, A297, A302, A335, A336, A337, A338, B25, B26, B27, B28, B29, B30, B56, B57, B58, B59, B99, B100, B101, B174, B175, B194,B195, B196, B197, B220, B221, B283, B284, B285, B286, B295, B296, B297,B298, B299, B300, B337, B338. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. FINAL STRUCTURE HAS NO RESIDUES IN THE DISALLOWED REGION OF THE RAMACHANDRAN PLOT AS DEFINED IN THE CCP4 PROCHECK PROGRAM.
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2552 | 966 | 5.11 % | RANDOM |
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Rwork | 0.1991 | - | - | - |
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obs | 0.2018 | 18907 | 90.13 % | - |
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原子変位パラメータ | Biso mean: 91.44 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -6.4458 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -6.4458 Å2 | 0 Å2 |
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3- | - | - | 12.8915 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.559 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.75→27.65 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5438 | 0 | 125 | 52 | 5615 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 | Restraint function | Weight |
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X-RAY DIFFRACTION | t_bond_d0.008 | 5766 | HARMONIC2 | X-RAY DIFFRACTION | t_angle_deg1.05 | 7871 | HARMONIC2 | X-RAY DIFFRACTION | t_dihedral_angle_d | 1920 | SINUSOIDAL2 | X-RAY DIFFRACTION | t_incorr_chiral_ct | | | | X-RAY DIFFRACTION | t_pseud_angle | | | | X-RAY DIFFRACTION | t_trig_c_planes | 169 | HARMONIC2 | X-RAY DIFFRACTION | t_gen_planes | 836 | HARMONIC5 | X-RAY DIFFRACTION | t_it | 5766 | HARMONIC20 | X-RAY DIFFRACTION | t_nbd | | | | X-RAY DIFFRACTION | t_omega_torsion2.28 | | | | X-RAY DIFFRACTION | t_other_torsion21.7 | | | | X-RAY DIFFRACTION | t_improper_torsion | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion | 720 | SEMIHARMONIC5 | X-RAY DIFFRACTION | t_sum_occupancies | | | | X-RAY DIFFRACTION | t_utility_distance | | | | X-RAY DIFFRACTION | t_utility_angle | | | | X-RAY DIFFRACTION | t_utility_torsion | | | | X-RAY DIFFRACTION | t_ideal_dist_contact | 6329 | SEMIHARMONIC4 | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.75→2.9 Å / Total num. of bins used: 10
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2701 | 129 | 5.55 % |
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Rwork | 0.2502 | 2196 | - |
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all | 0.2514 | 2325 | - |
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obs | - | - | 90.13 % |
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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 | 3.498 | -1.6633 | -2.8108 | 3.1029 | 2.7613 | 8.1777 | -0.0867 | -0.2501 | -0.2611 | -0.2785 | -0.3725 | 0.4117 | -1.0488 | -0.3604 | 0.4592 | -0.1442 | 0.0637 | -0.1138 | -0.2011 | -0.0505 | -0.2658 | -14.7523 | 6.5015 | 14.6195 | 2 | 3.2919 | 2.9125 | -0.5094 | 4.9133 | 0.5156 | 5.0515 | 0.3626 | -0.5387 | 0.3142 | -0.0661 | -0.3964 | 0.0038 | -0.6702 | 0.1179 | 0.0339 | 0.1355 | -0.4144 | 0.0593 | -0.088 | -0.138 | -0.3899 | 7.3093 | 32.5094 | 19.3979 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | A1 - A357 | 2 | X-RAY DIFFRACTION | 2 | B1 - B355 |
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