ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データ収集 | PHASER | | 位相決定 | REFMAC | 5.2.0019精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | |
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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 2OY7 解像度: 1.75→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.657 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.147 / 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 | 0.27388 | 3435 | 10 % | RANDOM |
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Rwork | 0.22311 | - | - | - |
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obs | 0.22808 | 30820 | 99.77 % | - |
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all | - | 30820 | - | - |
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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: 1.2 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso mean: 9.558 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 4.24 Å2 | 0 Å2 | -0.11 Å2 |
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2- | - | -2.1 Å2 | 0 Å2 |
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3- | - | - | -2.21 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.75→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2394 | 0 | 26 | 249 | 2669 |
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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_d0.014 | 0.022 | 2461 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 1681 | X-RAY DIFFRACTION | r_angle_refined_deg1.504 | 1.997 | 3307 | X-RAY DIFFRACTION | r_angle_other_deg2.277 | 3 | 4186 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.97 | 5 | 325 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.954 | 26.782 | 87 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg17.404 | 15 | 492 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg22 | 15 | 5 | X-RAY DIFFRACTION | r_chiral_restr0.084 | 0.2 | 402 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 2666 | X-RAY DIFFRACTION | r_gen_planes_other0.002 | 0.02 | 418 | X-RAY DIFFRACTION | r_nbd_refined0.209 | 0.2 | 414 | X-RAY DIFFRACTION | r_nbd_other0.216 | 0.2 | 1728 | X-RAY DIFFRACTION | r_nbtor_refined0.173 | 0.2 | 1179 | X-RAY DIFFRACTION | r_nbtor_other0.094 | 0.2 | 1440 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.185 | 0.2 | 216 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.233 | 0.2 | 32 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.22 | 0.2 | 74 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.2 | 0.2 | 20 | X-RAY DIFFRACTION | r_mcbond_it1.233 | 1.5 | 2033 | X-RAY DIFFRACTION | r_mcbond_other0.101 | 1.5 | 658 | X-RAY DIFFRACTION | r_mcangle_it1.096 | 2 | 2545 | X-RAY DIFFRACTION | r_scbond_it2.438 | 3 | 1012 | X-RAY DIFFRACTION | r_scangle_it3.379 | 4.5 | 757 | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.75→1.795 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.325 | 255 | - |
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Rwork | 0.299 | 2191 | - |
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obs | - | - | 97.18 % |
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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 | 0.4353 | 0.0944 | -0.2023 | 2.3004 | -0.5131 | 1.7207 | -0.0762 | -0.1471 | 0.0148 | -0.3135 | -0.0368 | -0.0385 | 0.1686 | 0.0717 | 0.113 | -0.163 | -0.0024 | -0.0383 | 0.0404 | -0.0001 | 0.024 | 9.6703 | 6.3938 | 33.5718 | 2 | 0.4167 | -0.004 | -0.1868 | 1.4328 | 0.9552 | 2.8505 | -0.012 | 0.0552 | 0.0435 | 0.0568 | -0.0756 | -0.2108 | 0.0259 | -0.0603 | 0.0876 | -0.0009 | 0.0039 | 0.0092 | -0.1477 | 0.0067 | -0.1081 | 6.6909 | 10.2276 | 1.3758 | 3 | 0.2478 | 0.1743 | 0.0549 | 1.5208 | -0.1903 | 1.9094 | -0.0812 | 0.0405 | -0.0555 | 0.0321 | 0.0953 | 0.185 | 0.2015 | -0.0165 | -0.0141 | -0.1145 | -0.0146 | 0.0371 | 0.0563 | 0.0217 | 0.033 | 16.1551 | -5.3394 | -31.8819 |
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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 | AA28 - 118 | 6 - 96 | 2 | X-RAY DIFFRACTION | 2 | AA119 - 209 | 97 - 187 | 3 | X-RAY DIFFRACTION | 3 | AA210 - 342 | 188 - 320 | | | | | | |
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