ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | HKL-3000 | | 位相決定 | MLPHARE | | 位相決定 | 直接法 | | モデル構築 | SHELXD | | 位相決定 | RESOLVE | | モデル構築 | Coot | | モデル構築 | REFMAC | 5.5.0054精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | 直接法 | | 位相決定 | RESOLVE | | 位相決定 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 1.78→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.94 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / 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 | 0.2198 | 982 | 5.1 % | RANDOM |
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Rwork | 0.17989 | - | - | - |
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all | 0.1819 | 19143 | - | - |
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obs | 0.1819 | 19143 | 99.44 % | - |
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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: 28.204 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.01 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.41 Å2 | 0 Å2 |
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3- | - | - | 0.4 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.78→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1330 | 0 | 16 | 142 | 1488 |
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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_d0.015 | 0.022 | 1415 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.373 | 1.985 | 1898 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg4.523 | 5 | 192 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg39.573 | 27.536 | 69 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.194 | 15 | 273 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.438 | 15 | 2 | X-RAY DIFFRACTION | r_chiral_restr0.096 | 0.2 | 209 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 1059 | X-RAY DIFFRACTION | r_gen_planes_other | | | 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_it0.879 | 1.5 | 895 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.585 | 2 | 1415 | X-RAY DIFFRACTION | r_scbond_it2.779 | 3 | 520 | X-RAY DIFFRACTION | r_scangle_it4.409 | 4.5 | 475 | 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: 1.78→1.827 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.311 | 66 | - |
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Rwork | 0.247 | 1312 | - |
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obs | - | 1378 | 99.14 % |
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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 | 0.935 | 2.9033 | -0.8978 | 9.2069 | -2.5433 | 1.1736 | -0.1061 | 0.0974 | 0.059 | -0.3094 | 0.2476 | 0.1137 | 0.1215 | -0.1612 | -0.1415 | 0.021 | -0.0205 | -0.0306 | 0.0282 | 0.0365 | 0.0701 | 11.9625 | 46.2955 | -3.9623 | 2 | 1.5465 | -0.5317 | 0.0702 | 2.7154 | -1.0316 | 1.6649 | -0.0172 | 0.0692 | -0.0574 | -0.1817 | 0.1235 | -0.0817 | 0.2011 | -0.0581 | -0.1063 | 0.0485 | -0.016 | -0.0166 | 0.0149 | -0.005 | 0.028 | 8.3397 | 20.1032 | 9.884 | 3 | 2.293 | 0.4652 | -0.7699 | 2.4539 | -1.9211 | 3.1087 | -0.0596 | -0.2531 | -0.0978 | 0.0684 | 0.0751 | -0.2299 | 0.1649 | 0.0456 | -0.0155 | 0.0372 | 0.0239 | -0.0304 | 0.0425 | -0.0061 | 0.051 | 13.1243 | 16.7598 | 21.3262 | 4 | 3.5932 | -0.313 | -0.9604 | 4.9201 | -2.9912 | 3.7599 | 0.0329 | 0.0785 | 0.0669 | -0.1986 | 0.0598 | -0.1306 | 0.2131 | 0.1116 | -0.0927 | 0.0204 | 0.0106 | 0.0125 | 0.0224 | -0.0128 | 0.0644 | 20.0168 | 34.6533 | 3.0733 | 5 | 6.7201 | 3.6418 | -2.4503 | 3.8946 | -5.5739 | 10.4001 | 0.0766 | -0.3182 | 0.0607 | 0.1669 | -0.2362 | -0.1042 | -0.203 | 0.3066 | 0.1596 | 0.164 | 0.0075 | -0.0434 | 0.0519 | -0.0764 | 0.1848 | 24.445 | 45.5562 | 12.4177 | 6 | 3.1162 | 0.5277 | -1.201 | 2.2763 | -0.5104 | 3.2489 | 0.1314 | -0.5049 | 0.1393 | 0.2541 | -0.0853 | -0.222 | -0.2709 | 0.1428 | -0.0462 | 0.0611 | 0.0005 | -0.0243 | 0.1012 | -0.0281 | 0.036 | 10.318 | 28.3291 | 25.5941 | 7 | 3.3654 | 1.9744 | -0.5065 | 4.1439 | -0.749 | 1.193 | -0.0077 | -0.1191 | -0.0305 | 0.0227 | 0.0491 | -0.0182 | 0.0283 | -0.1473 | -0.0414 | 0.0105 | 0.0111 | -0.0021 | 0.0511 | 0.0064 | 0.0024 | 1.6705 | 22.2562 | 20.4089 | 8 | 4.0181 | -0.2627 | -0.0095 | 9.2949 | -6.1333 | 4.8382 | 0.0645 | -0.1717 | 0.3978 | 0.5939 | -0.0708 | -0.0957 | -0.4394 | -0.0463 | 0.0063 | 0.0593 | 0.0024 | 0.008 | 0.0224 | -0.0104 | 0.0434 | 12.4508 | 44.034 | 13.7844 |
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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 | A1 - 24 | 2 | X-RAY DIFFRACTION | 2 | A25 - 55 | 3 | X-RAY DIFFRACTION | 3 | A56 - 77 | 4 | X-RAY DIFFRACTION | 4 | A78 - 92 | 5 | X-RAY DIFFRACTION | 5 | B8 - 24 | 6 | X-RAY DIFFRACTION | 6 | B25 - 55 | 7 | X-RAY DIFFRACTION | 7 | B56 - 77 | 8 | X-RAY DIFFRACTION | 8 | B78 - 91 | | | | | | | | |
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