ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0267精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHASER | | 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: 2WHV 解像度: 2.097→41.671 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.875 / SU ML: 0.159 / 交差検証法: FREE R-VALUE / ESU R: 0.196 / ESU R Free: 0.187 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2665 | 891 | 5.073 % |
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Rwork | 0.2108 | 16674 | - |
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all | 0.214 | - | - |
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obs | - | 17565 | 98.475 % |
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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 BULK SOLVENT |
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原子変位パラメータ | Biso mean: 40.331 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.921 Å2 | -0 Å2 | -0 Å2 |
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2- | - | 1.921 Å2 | -0 Å2 |
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3- | - | - | -3.843 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.097→41.671 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1613 | 0 | 9 | 148 | 1770 |
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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 | 0.013 | 1675 | X-RAY DIFFRACTION | r_bond_other_d0.003 | 0.017 | 1543 | X-RAY DIFFRACTION | r_angle_refined_deg1.857 | 1.643 | 2294 | X-RAY DIFFRACTION | r_angle_other_deg1.396 | 1.576 | 3546 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.924 | 5 | 212 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.348 | 23.723 | 94 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.058 | 15 | 258 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg17.002 | 15 | 9 | X-RAY DIFFRACTION | r_chiral_restr0.081 | 0.2 | 225 | X-RAY DIFFRACTION | r_gen_planes_refined0.01 | 0.02 | 1959 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 403 | X-RAY DIFFRACTION | r_nbd_refined0.227 | 0.2 | 332 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.186 | 0.2 | 1520 | X-RAY DIFFRACTION | r_nbtor_refined0.172 | 0.2 | 826 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.082 | 0.2 | 918 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.207 | 0.2 | 124 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.091 | 0.2 | 2 | X-RAY DIFFRACTION | r_metal_ion_refined0.209 | 0.2 | 38 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.201 | 0.2 | 12 | X-RAY DIFFRACTION | r_nbd_other0.151 | 0.2 | 42 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.218 | 0.2 | 6 | X-RAY DIFFRACTION | r_mcbond_it1.773 | 2.6 | 833 | X-RAY DIFFRACTION | r_mcbond_other1.774 | 2.596 | 832 | X-RAY DIFFRACTION | r_mcangle_it2.797 | 3.885 | 1041 | X-RAY DIFFRACTION | r_mcangle_other2.796 | 3.889 | 1042 | X-RAY DIFFRACTION | r_scbond_it2.011 | 2.855 | 842 | X-RAY DIFFRACTION | r_scbond_other2.008 | 2.847 | 840 | X-RAY DIFFRACTION | r_scangle_it3.218 | 4.177 | 1250 | X-RAY DIFFRACTION | r_scangle_other3.219 | 4.176 | 1250 | X-RAY DIFFRACTION | r_lrange_it6.67 | 31.887 | 1906 | X-RAY DIFFRACTION | r_lrange_other6.252 | 31.171 | 1856 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.097-2.151 | 0.405 | 46 | 0.307 | 1060 | X-RAY DIFFRACTION | 86.2042 | 2.151-2.21 | 0.403 | 50 | 0.28 | 1141 | X-RAY DIFFRACTION | 95.0519 | 2.21-2.274 | 0.33 | 52 | 0.263 | 1149 | X-RAY DIFFRACTION | 98.9292 | 2.274-2.344 | 0.375 | 52 | 0.241 | 1102 | X-RAY DIFFRACTION | 100 | 2.344-2.421 | 0.338 | 72 | 0.24 | 1100 | X-RAY DIFFRACTION | 100 | 2.421-2.506 | 0.413 | 65 | 0.259 | 1013 | X-RAY DIFFRACTION | 100 | 2.506-2.6 | 0.191 | 49 | 0.236 | 1041 | X-RAY DIFFRACTION | 100 | 2.6-2.706 | 0.347 | 53 | 0.237 | 1007 | X-RAY DIFFRACTION | 100 | 2.706-2.827 | 0.305 | 39 | 0.239 | 934 | X-RAY DIFFRACTION | 100 | 2.827-2.964 | 0.303 | 46 | 0.235 | 921 | X-RAY DIFFRACTION | 99.8967 | 2.964-3.124 | 0.288 | 52 | 0.204 | 883 | X-RAY DIFFRACTION | 100 | 3.124-3.314 | 0.211 | 41 | 0.189 | 816 | X-RAY DIFFRACTION | 100 | 3.314-3.542 | 0.238 | 55 | 0.201 | 766 | X-RAY DIFFRACTION | 100 | 3.542-3.825 | 0.279 | 44 | 0.196 | 740 | X-RAY DIFFRACTION | 100 | 3.825-4.189 | 0.268 | 40 | 0.165 | 675 | X-RAY DIFFRACTION | 100 | 4.189-4.681 | 0.166 | 43 | 0.148 | 621 | X-RAY DIFFRACTION | 99.5502 | 4.681-5.402 | 0.214 | 25 | 0.174 | 583 | X-RAY DIFFRACTION | 99.6721 | 5.402-6.607 | 0.235 | 30 | 0.196 | 472 | X-RAY DIFFRACTION | 99.6032 | 6.607-9.307 | 0.199 | 27 | 0.196 | 392 | X-RAY DIFFRACTION | 99.0544 | 9.307-41.67 | 0.27 | 10 | 0.256 | 258 | X-RAY DIFFRACTION | 97.1014 |
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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 | 2.1418 | -0.1159 | -0.6903 | 0.5023 | 1.4831 | 8.8269 | -0.0419 | 0.0532 | -0.3247 | 0.0435 | -0.0409 | 0.0613 | 0.624 | 0.023 | 0.0829 | 0.0628 | 0.0346 | -0.0056 | 0.1402 | -0.023 | 0.1055 | 3.4 | 4.424 | -49.6238 | 2 | 0.8894 | 0.0747 | 1.2684 | 1.2625 | 1.7617 | 7.5736 | -0.0242 | 0.1074 | 0.0551 | 0.2112 | -0.1125 | 0.0983 | 0.2892 | -0.7042 | 0.1367 | 0.0422 | -0.0483 | 0.0265 | 0.2152 | -0.0327 | 0.0561 | 2.3323 | 15.9494 | -2.6669 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLA1 - 101 | 2 | X-RAY DIFFRACTION | 1 | ALLA302 | 3 | X-RAY DIFFRACTION | 1 | ALLA303 - 304 | 4 | X-RAY DIFFRACTION | 2 | ALLA102 - 206 | 5 | X-RAY DIFFRACTION | 2 | ALLA305 - 306 | 6 | X-RAY DIFFRACTION | 2 | ALLA301 | 7 | X-RAY DIFFRACTION | 2 | ALLA307 | | | | | | | | | | | | | | |
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