ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | REFMAC | | 精密化 | | PDB_EXTRACT | 3.006 | データ抽出 | | 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 | 開始モデル: PDB ENTRY 3G2M 解像度: 2.95→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.885 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.228 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.835 / SU B: 33.846 / SU ML: 0.303 / SU R Cruickshank DPI: 0.372 / SU Rfree: 0.437 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424 / 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 | 0.259 | 684 | 5 % | RANDOM |
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Rwork | 0.209 | - | - | - |
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obs | 0.211 | 13628 | 96.96 % | - |
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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 max: 80.93 Å2 / Biso mean: 50.76 Å2 / Biso min: 22.18 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.82 Å2 | 0 Å2 | -0.22 Å2 |
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2- | - | 3.65 Å2 | 0 Å2 |
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3- | - | - | -0.94 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.95→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3703 | 0 | 45 | 9 | 3757 |
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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 | 0.022 | 3821 | X-RAY DIFFRACTION | r_angle_refined_deg1.49 | 1.992 | 5176 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.728 | 5 | 481 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.165 | 22.485 | 169 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg18.691 | 15 | 613 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg20.24 | 15 | 43 | X-RAY DIFFRACTION | r_chiral_restr0.093 | 0.2 | 592 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 2900 | X-RAY DIFFRACTION | r_nbd_refined0.226 | 0.2 | 1693 | X-RAY DIFFRACTION | r_nbtor_refined0.311 | 0.2 | 2544 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.16 | 0.2 | 133 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.16 | 0.2 | 30 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.073 | 0.2 | 2 | X-RAY DIFFRACTION | r_mcbond_it0.628 | 1.5 | 2490 | X-RAY DIFFRACTION | r_mcangle_it1.089 | 2 | 3873 | X-RAY DIFFRACTION | r_scbond_it1.304 | 3 | 1474 | X-RAY DIFFRACTION | r_scangle_it2.226 | 4.5 | 1302 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.95→3.027 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.371 | 54 | - |
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Rwork | 0.306 | 881 | - |
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all | - | 935 | - |
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obs | - | - | 89.47 % |
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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 | 3.0756 | -0.1826 | 0.3302 | 1.9192 | 0.2069 | 1.3771 | -0.0262 | -0.0247 | 0.1836 | 0.0704 | -0.0192 | -0.225 | -0.0849 | 0.0437 | 0.0454 | -0.0676 | -0.0216 | -0.0067 | -0.0713 | 0.0215 | -0.0222 | 22.4226 | 65.2342 | 34.8358 | 2 | 8.8977 | -3.0984 | -0.3993 | 2.7326 | -0.3742 | 0.978 | 0.1646 | 0.1945 | 1.4121 | 0.0053 | -0.051 | 0.2914 | -0.5421 | -0.2087 | -0.1136 | 0.1066 | 0.1081 | -0.0042 | 0.0525 | 0.0723 | 0.2498 | -3.6566 | 76.6584 | 17.8068 | 3 | 4.9115 | -0.5069 | -3.0768 | 1.1626 | 2.0573 | 4.6536 | -0.3533 | -0.3262 | -0.4192 | 0.3257 | 0.2281 | -0.1844 | 0.8806 | 0.7226 | 0.1252 | 0.1168 | 0.1551 | 0.0644 | 0.0976 | 0.0545 | 0.0368 | 22.9474 | 52.92 | 9.7304 | 4 | 3.2246 | 0.1912 | -0.2438 | 0.3538 | -0.0687 | 1.3204 | -0.0128 | 0.0732 | -0.2378 | -0.0022 | -0.0299 | -0.0627 | 0.1224 | -0.1334 | 0.0427 | -0.0046 | -0.0251 | 0.0191 | -0.0069 | -0.0268 | -0.0711 | -13.3234 | 50.946 | 16.3421 |
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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 | A47 - 175 | 2 | X-RAY DIFFRACTION | 1 | A235 - 273 | 3 | X-RAY DIFFRACTION | 2 | B8 - 32 | 4 | X-RAY DIFFRACTION | 2 | B206 - 234 | 5 | X-RAY DIFFRACTION | 2 | A176 - 205 | 6 | X-RAY DIFFRACTION | 3 | A8 - 37 | 7 | X-RAY DIFFRACTION | 3 | A206 - 234 | 8 | X-RAY DIFFRACTION | 3 | B176 - 205 | 9 | X-RAY DIFFRACTION | 4 | B47 - 175 | 10 | X-RAY DIFFRACTION | 4 | B235 - 273 | | | | | | | | | | |
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