ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.1.13精密化 | DENZO | | データ削減 | SCALEPACK | | データスケーリング | AMoRE | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.5→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.355 / SU ML: 0.052 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.102 / 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 | 0.239 | 489 | 4.9 % | RANDOM |
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Rwork | 0.204 | - | - | - |
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obs | 0.206 | 9590 | 93.9 % | - |
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all | - | 9590 | - | - |
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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: 15.01 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.04 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 2.69 Å2 | 0 Å2 |
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3- | - | - | -0.65 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.5→15 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 536 | 5 | 170 | 711 |
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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 | 0.02 | 598 | X-RAY DIFFRACTION | r_bond_other_d0.003 | 0.02 | 264 | X-RAY DIFFRACTION | r_angle_refined_deg1.987 | 2.09 | 892 | X-RAY DIFFRACTION | r_angle_other_deg1.135 | 2 | 654 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_2_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_3_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_4_deg | | | X-RAY DIFFRACTION | r_chiral_restr0.077 | 0.2 | 72 | X-RAY DIFFRACTION | r_gen_planes_refined0.018 | 0.02 | 284 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.141 | 0.2 | 55 | X-RAY DIFFRACTION | r_nbd_other0.267 | 0.2 | 328 | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other0.159 | 0.2 | 143 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.162 | 0.2 | 92 | 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_refined0.101 | 0.2 | 8 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.181 | 0.2 | 28 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.22 | 0.2 | 47 | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_mcbond_it | | | X-RAY DIFFRACTION | r_mcangle_it | | | X-RAY DIFFRACTION | r_scbond_it2.232 | 3 | 598 | X-RAY DIFFRACTION | r_scangle_it2.954 | 4.5 | 892 | X-RAY DIFFRACTION | r_rigid_bond_restr1.653 | 2 | 598 | X-RAY DIFFRACTION | r_sphericity_free2.794 | 2 | 175 | X-RAY DIFFRACTION | r_sphericity_bonded2.406 | 2 | 536 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.5→1.54 Å / Total num. of bins used: 20 / | Rfactor | 反射数 |
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Rfree | 0.268 | 30 |
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Rwork | 0.174 | 637 |
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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 | 2.0786 | 0.061 | -0.0748 | 0.3326 | -0.0446 | 0.1001 | -0.0028 | 0.0516 | -0.0428 | 0.0514 | 0.0041 | -0.0282 | 0.0188 | 0.03 | -0.0014 | 0.0991 | -0.0038 | -0.0082 | 0.0004 | -0.0043 | 0.0718 | 9.4124 | 2.1378 | 7.9253 | 2 | -0.0517 | 0.3557 | -0.6334 | 0.1413 | -0.5311 | 2.2258 | 0.0805 | -0.0351 | 0.0299 | 0.0423 | 0.0493 | 0.0526 | -0.0628 | 0.0688 | -0.1298 | 0.0898 | 0 | 0.0115 | 0.0134 | -0.0034 | 0.0825 | 22.7919 | 1.6144 | 20.0751 |
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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 | AA1 - 14 | 1 - 13 | 2 | X-RAY DIFFRACTION | 2 | BB1 - 14 | 1 - 13 | | | | |
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精密化 | *PLUS 最低解像度: 15 Å / % reflection Rfree: 5 % |
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溶媒の処理 | *PLUS |
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原子変位パラメータ | *PLUS |
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拘束条件 | *PLUS Refine-ID | タイプ | Dev ideal |
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X-RAY DIFFRACTION | r_bond_d0.017 | X-RAY DIFFRACTION | r_angle_d | X-RAY DIFFRACTION | r_angle_deg1.98 | | | |
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.275 / Rfactor Rwork: 0.176 |
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