ソフトウェア | 名称 | バージョン | 分類 |
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Blu-Ice | | データ収集 | PHASER | | 位相決定 | REFMAC | 5.5.0109精密化 | XDS | | データ削減 | XSCALE | | 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 3MBQ, orthorhombic crystal form 解像度: 1.45→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.879 / SU ML: 0.033 / Isotropic thermal model: isotropic, TLS / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.167 | 1475 | 5.1 % | RANDOM |
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Rwork | 0.15 | - | - | - |
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all | 0.151 | 29210 | - | - |
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obs | 0.151 | 29143 | 99.8 % | - |
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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: 14.88 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.05 Å2 | -0.02 Å2 | 0 Å2 |
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2- | - | -0.05 Å2 | 0 Å2 |
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3- | - | - | 0.07 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.45→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1036 | 0 | 4 | 181 | 1221 |
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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 | 0.022 | 1097 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 765 | X-RAY DIFFRACTION | r_angle_refined_deg1.683 | 1.996 | 1496 | X-RAY DIFFRACTION | r_angle_other_deg0.978 | 3 | 1864 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.378 | 5 | 150 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg29.934 | 22.917 | 48 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg10.053 | 15 | 182 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.104 | 15 | 13 | X-RAY DIFFRACTION | r_chiral_restr0.106 | 0.2 | 174 | X-RAY DIFFRACTION | r_gen_planes_refined0.007 | 0.021 | 1248 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 221 | 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_it1.091 | 1.5 | 707 | X-RAY DIFFRACTION | r_mcbond_other0.325 | 1.5 | 291 | X-RAY DIFFRACTION | r_mcangle_it1.856 | 2 | 1137 | X-RAY DIFFRACTION | r_scbond_it2.664 | 3 | 390 | X-RAY DIFFRACTION | r_scangle_it4.233 | 4.5 | 352 | 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: 1.45→1.49 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.26 | 122 | - |
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Rwork | 0.231 | 2073 | - |
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obs | - | - | 99.95 % |
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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 | 1.5275 | -0.3829 | -0.5398 | 1.4641 | 0.1972 | 0.8375 | 0.0882 | -0.0646 | 0.0484 | 0.1725 | 0.0684 | 0.25 | -0.1332 | -0.1791 | -0.1566 | 0.0758 | 0.0461 | 0.0958 | 0.0914 | 0.0265 | 0.1211 | 19.542 | -5.768 | 3.308 | 2 | 0.4785 | -0.9251 | 1.1692 | 2.6503 | -0.5992 | 1.9752 | 0.0285 | -0.0458 | 0.0108 | -0.1729 | 0.165 | 0.1953 | -0.1408 | -0.2396 | -0.1935 | 0.0374 | 0.0164 | 0.0266 | 0.0887 | 0.087 | 0.1202 | 21.333 | -6.834 | -15.478 | 3 | 0.4174 | -0.115 | -0.1033 | 0.837 | 0.3516 | 0.7998 | 0.0679 | -0.0514 | 0.0834 | 0.0036 | 0.0655 | 0.0453 | -0.0385 | -0.0635 | -0.1334 | 0.0506 | 0.0095 | 0.0327 | 0.0601 | 0.0083 | 0.0751 | 29.108 | -9.969 | -4.792 | 4 | 2.8182 | -1.5805 | -0.7458 | 0.1031 | 0.6411 | 3.503 | 0.1589 | -0.1203 | 0.0121 | -0.0835 | 0.0464 | 0.081 | 0.1646 | -0.5716 | -0.2053 | 0.0588 | -0.012 | 0.0181 | 0.1166 | 0.0937 | 0.1264 | 18.815 | -11.085 | -14.465 | 5 | 0.8943 | -0.2055 | 0.4096 | 0.593 | -0.1648 | 0.8279 | -0.0168 | -0.165 | 0.0024 | 0.176 | 0.0963 | -0.0989 | -0.0268 | 0.0022 | -0.0795 | 0.0578 | -0.0022 | -0.0314 | 0.0708 | -0.0393 | 0.0546 | 46.27 | -18.472 | 6.866 |
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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 | A8 - 34 | 2 | X-RAY DIFFRACTION | 2 | A35 - 53 | 3 | X-RAY DIFFRACTION | 3 | A54 - 110 | 4 | X-RAY DIFFRACTION | 4 | A111 - 124 | 5 | X-RAY DIFFRACTION | 5 | A125 - 151 | | | | | |
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