ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5 | 精密化 | XDS | | データ削減 | XDS | | データスケーリング | CNS | | 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: 1LNG 解像度: 2.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 18.786 / SU ML: 0.364 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.31 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.29616 | 783 | 5 % | RANDOM |
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Rwork | 0.2531 | - | - | - |
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obs | 0.2552 | 14857 | 98.9 % | - |
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all | - | 15640 | - | - |
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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: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 37.874 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.44 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 2.44 Å2 | 0 Å2 |
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3- | - | - | -4.88 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.6→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 2169 | 0 | 139 | 2308 |
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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_d0.02 | 0.021 | 2427 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 819 | X-RAY DIFFRACTION | r_angle_refined_deg3.226 | 3 | 3787 | X-RAY DIFFRACTION | r_angle_other_deg2.024 | 3 | 2141 | 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_restr0.114 | 0.2 | 404 | X-RAY DIFFRACTION | r_gen_planes_refined0.011 | 0.02 | 1061 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.32 | 0.3 | 1220 | X-RAY DIFFRACTION | r_nbd_other0.36 | 0.3 | 1418 | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other0.026 | 0.5 | 8 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.246 | 0.5 | 208 | X-RAY DIFFRACTION | r_xyhbond_nbd_other0.128 | 0.5 | 10 | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.243 | 0.3 | 21 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.159 | 0.3 | 8 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.274 | 0.5 | 7 | 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_it | | | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it | | | X-RAY DIFFRACTION | r_scbond_it2.05 | 3 | 2427 | X-RAY DIFFRACTION | r_scangle_it3.007 | 4.5 | 3787 | 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: 2.6→2.666 Å / Total num. of bins used: 20 / | Rfactor | 反射数 |
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Rfree | 0.37 | 40 |
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Rwork | 0.458 | 1051 |
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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 | 6.1014 | -2.5542 | 1.3466 | 1.9712 | -2.33 | 3.2089 | -0.0166 | 0.0238 | 0.0507 | 0.0454 | -0.1358 | 0.0555 | -0.2436 | -0.0354 | 0.1524 | 0.3863 | -0.0011 | 0.0861 | 0.3913 | -0.0444 | 0.3186 | 46.6659 | -6.8158 | 113.3783 | 2 | 3.0243 | -1.0789 | 0.8167 | 1.1813 | -2.3122 | 4.2537 | 0.1438 | 0.3627 | 0.1684 | 0.0379 | -0.2062 | 0.1296 | 0.0607 | 0.6235 | 0.0624 | 0.3539 | -0.0443 | 0.0411 | 0.3935 | 0.0532 | 0.4392 | 38.7391 | 2.7178 | 96.9195 | 3 | 10.7175 | 2.4234 | 5.2098 | 4.393 | -1.7102 | 1.9753 | -0.0868 | 0.32 | 0.6706 | -0.4278 | 0.5603 | 0.8108 | 0.1144 | -0.6856 | -0.4736 | 0.3049 | 0.0177 | 0.2039 | 0.7776 | 0.1161 | 0.2935 | 20.0199 | 5.0654 | 102.324 | 4 | -2.0784 | -1.4214 | 2.8585 | 2.4155 | -5.6027 | 4.6705 | 0.3216 | -0.5064 | -0.3469 | -0.9661 | 0.2097 | 0.156 | 1.3979 | -0.5524 | -0.5312 | 0.552 | -0.1139 | -0.0225 | 0.8347 | 0.1573 | 0.6567 | 9.2647 | 5.9915 | 81.3993 | 5 | 4.9218 | -2.4501 | 2.3653 | 2.1865 | -2.726 | 1.1608 | 0.0493 | -0.0781 | -0.2088 | -0.1092 | 0.0312 | 0.1426 | -0.0954 | -0.2693 | -0.0804 | 0.3249 | 0.0353 | 0.0567 | 0.4425 | -0.0191 | 0.4332 | 24.0175 | 16.7558 | 74.238 |
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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 | A138 - 147 | 2 | X-RAY DIFFRACTION | 1 | A232 - 238 | 3 | X-RAY DIFFRACTION | 2 | A182 - 197 | 4 | X-RAY DIFFRACTION | 2 | A224 - 231 | 5 | X-RAY DIFFRACTION | 3 | A148 - 152 | 6 | X-RAY DIFFRACTION | 3 | A178 - 181 | 7 | X-RAY DIFFRACTION | 4 | A153 - 177 | 8 | X-RAY DIFFRACTION | 5 | A198 - 223 | | | | | | | | |
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