ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0019精密化 | DENZO | | データ削減 | SCALA | | データスケーリング | SOLVE | | 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: 1.6→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.85 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.081 / 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 | 0.20645 | 2234 | 10.1 % | RANDOM |
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Rwork | 0.17147 | - | - | - |
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obs | 0.17495 | 19846 | 99.5 % | - |
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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: BABINET MODEL WITH MASK |
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原子変位パラメータ | Biso mean: 32.369 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 2.5 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -1 Å2 | 0 Å2 |
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3- | - | - | -1.51 Å2 |
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Refine analyze | Luzzati coordinate error free: 0.08 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→20 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 907 | 0 | 20 | 158 | 1085 |
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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_d0.013 | 0.022 | 954 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 622 | X-RAY DIFFRACTION | r_angle_refined_deg1.355 | 1.992 | 1298 | X-RAY DIFFRACTION | r_angle_other_deg1.798 | 3.008 | 1534 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.609 | 5 | 116 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg38.688 | 27.111 | 45 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.954 | 15 | 162 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg9.103 | 15 | 2 | X-RAY DIFFRACTION | r_chiral_restr0.076 | 0.2 | 147 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 1046 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 162 | X-RAY DIFFRACTION | r_nbd_refined0.224 | 0.2 | 217 | X-RAY DIFFRACTION | r_nbd_other0.185 | 0.2 | 603 | X-RAY DIFFRACTION | r_nbtor_refined0.18 | 0.2 | 477 | X-RAY DIFFRACTION | r_nbtor_other0.091 | 0.2 | 469 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.185 | 0.2 | 108 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.261 | 0.2 | 11 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.17 | 0.2 | 30 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.14 | 0.2 | 22 | X-RAY DIFFRACTION | r_mcbond_it0.798 | 1.5 | 760 | X-RAY DIFFRACTION | r_mcbond_other0.199 | 1.5 | 233 | X-RAY DIFFRACTION | r_mcangle_it1.013 | 2 | 957 | X-RAY DIFFRACTION | r_scbond_it1.513 | 3 | 418 | X-RAY DIFFRACTION | r_scangle_it1.968 | 4.5 | 341 | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.6→1.641 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.205 | 166 | - |
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Rwork | 0.191 | 1442 | - |
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obs | - | 1442 | 99.57 % |
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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 | 1.5644 | -0.7131 | 0.7883 | 2.8798 | -2.1284 | 4.9897 | -0.0279 | 0.0382 | 0.2414 | 0.1621 | -0.2743 | -0.3601 | -0.416 | 0.6279 | 0.3022 | -0.3563 | -0.0691 | -0.0238 | -0.1821 | 0.0241 | -0.1738 | 11.408 | 11.725 | -4.917 | 2 | 14.4987 | 0.1734 | -5.0735 | 1.4905 | 0.7752 | 2.8145 | -0.4248 | 0.4353 | -0.5238 | -0.2442 | 0.2436 | -0.2549 | 0.4237 | -0.0292 | 0.1812 | -0.1521 | -0.2236 | 0.0081 | 0.1391 | -0.1039 | -0.0849 | 19.56 | 18.703 | 9.203 | 3 | 5.4872 | 1.6413 | 1.5349 | 8.7289 | 1.8479 | 6.7579 | -0.1126 | -0.1397 | 0.3552 | -0.004 | -0.0213 | -0.1606 | -0.8839 | 0.3305 | 0.1339 | -0.2494 | -0.0569 | -0.0074 | -0.1862 | -0.0156 | -0.2138 | 7.065 | 15.669 | 4.537 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA3 - 69 | 3 - 69 | 2 | X-RAY DIFFRACTION | 2 | AA70 - 88 | 70 - 88 | 3 | X-RAY DIFFRACTION | 3 | AA89 - 119 | 89 - 119 | | | | | | |
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