ソフトウェア | 名称 | バージョン | 分類 |
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MAR345 | | データ収集 | PHASER | | 位相決定 | REFMAC | 5.5.0066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 2IGO 解像度: 1.9→28.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.969 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.164 / 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 | 0.27116 | 2702 | 5 % | RANDOM |
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Rwork | 0.20622 | - | - | - |
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all | 0.20941 | 50826 | - | - |
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obs | 0.20941 | 50826 | 99.9 % | - |
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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: 12.137 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.79 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.79 Å2 | 0 Å2 |
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3- | - | - | 1.57 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→28.8 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4517 | 0 | 53 | 390 | 4960 |
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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_d0.022 | 0.022 | 4689 | X-RAY DIFFRACTION | r_bond_other_d0 | 0.02 | 4072 | X-RAY DIFFRACTION | r_angle_refined_deg1.919 | 1.96 | 6375 | X-RAY DIFFRACTION | r_angle_other_deg0.802 | 3 | 9519 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg7.313 | 5 | 570 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg38.895 | 24.464 | 224 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.625 | 15 | 753 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg14.215 | 15 | 27 | X-RAY DIFFRACTION | r_chiral_restr0.133 | 0.2 | 693 | X-RAY DIFFRACTION | r_gen_planes_refined0.01 | 0.021 | 5200 | X-RAY DIFFRACTION | r_gen_planes_other0 | 0.02 | 940 | 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_it0.966 | 1.5 | 2861 | X-RAY DIFFRACTION | r_mcbond_other0.33 | 1.5 | 1151 | X-RAY DIFFRACTION | r_mcangle_it1.524 | 2 | 4646 | X-RAY DIFFRACTION | r_scbond_it2.569 | 3 | 1828 | X-RAY DIFFRACTION | r_scangle_it3.736 | 4.5 | 1729 | 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: 1.9→2.002 Å / Total num. of bins used: 10
| Rfactor | 反射数 | %反射 |
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Rfree | 0.298 | 432 | - |
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Rwork | 0.236 | 7234 | - |
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obs | - | - | 99.87 % |
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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 | 0.9765 | 0.164 | 0.1422 | 1.2293 | -0.1083 | 1.0441 | 0.0094 | 0.0981 | 0.0169 | -0.0552 | -0.0054 | 0.0065 | -0.0322 | -0.0506 | -0.0041 | 0.0713 | 0.001 | -0.0081 | 0.0656 | -0.0002 | 0.0661 | 67.789 | 49.8806 | 21.8696 | 2 | 0.0795 | 0.1025 | -0.1178 | 0.1321 | -0.1521 | 0.1782 | -0.0048 | -0.0183 | -0.0102 | 0.0215 | 0.0151 | 0.0323 | -0.0068 | -0.0359 | -0.0103 | 0.0715 | -0.0009 | -0.0027 | 0.0671 | -0.007 | 0.0666 | 59.3099 | 45.8561 | 47.2107 | 3 | 2.2792 | -0.182 | -0.0866 | 0.8025 | -0.5395 | 1.0292 | 0.0044 | 0.0971 | 0.0933 | 0.0001 | -0.0084 | -0.2145 | -0.0822 | 0.2954 | 0.0039 | 0.0834 | 0.0001 | 0.0027 | 0.055 | -0.0085 | 0.0741 | 83.1682 | 66.5118 | 32.6825 | 4 | 1.3203 | -0.2904 | -0.0846 | 1.2702 | 0.2176 | 1.3404 | -0.0333 | -0.0026 | 0.0708 | -0.035 | 0.0004 | 0.0067 | -0.123 | 0.0044 | 0.0329 | 0.0842 | -0.0028 | 0.0155 | 0.0675 | 0.0234 | 0.0861 | 62.9919 | 75.9415 | 41.2492 | 5 | 0.6836 | -0.3173 | -0.2946 | 0.3543 | 0.3397 | 0.326 | 0.0091 | 0.0479 | -0.0741 | -0.0896 | -0.004 | 0.064 | 0.0624 | -0.049 | -0.005 | 0.0843 | -0.0134 | -0.0068 | 0.0857 | 0.0002 | 0.0827 | 68.1922 | 44.5522 | 21.6381 | 6 | 0.9212 | 0.0849 | -0.2702 | 1.1267 | 0.073 | 2.2533 | 0.0637 | -0.0195 | -0.189 | 0.0371 | -0.0127 | -0.0901 | 0.2556 | 0.1373 | -0.051 | 0.0668 | -0.004 | 0.0087 | 0.0603 | -0.0011 | 0.0972 | 80.112 | 39.7559 | 35.0471 | 7 | 1.1026 | -0.88 | 0.2401 | 1.3598 | -0.3201 | 0.2821 | 0.0205 | 0.0821 | 0.1816 | -0.0518 | -0.0431 | 0.0278 | -0.1679 | -0.1 | 0.0227 | 0.1163 | -0.0136 | -0.0043 | 0.1174 | -0.013 | 0.0807 | 51.5745 | 84.529 | 51.7414 | 8 | 2.2135 | -1.0309 | -0.094 | 0.8263 | 0.1659 | 0.2124 | 0.0199 | -0.0455 | -0.1273 | -0.0025 | -0.022 | 0.1071 | 0.0995 | -0.0587 | 0.002 | 0.1089 | -0.0108 | -0.0045 | 0.0975 | -0.0047 | 0.0544 | 55.8985 | 74.9725 | 47.1469 | 9 | 0.5592 | -0.4063 | 0.0736 | 1.0818 | 0.2069 | 0.2778 | -0.0286 | 0.0151 | -0.0675 | 0.057 | 0.0323 | -0.0266 | 0.066 | 0.0405 | -0.0036 | 0.0778 | -0.0118 | 0.0144 | 0.083 | 0.0187 | 0.0413 | 70.3761 | 49.9821 | 48.0838 | 10 | 0.398 | -0.2157 | -0.4268 | 0.4615 | 0.3852 | 0.9889 | -0.0162 | 0.016 | -0.0263 | -0.0215 | 0.0159 | -0.0433 | 0.0492 | 0.0506 | 0.0002 | 0.0464 | -0.0106 | -0.0087 | 0.0451 | 0.009 | 0.0673 | 77.8334 | 56.5146 | 39.7346 |
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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 | A46 - 85 | 2 | X-RAY DIFFRACTION | 2 | A86 - 173 | 3 | X-RAY DIFFRACTION | 3 | A174 - 205 | 4 | X-RAY DIFFRACTION | 4 | A206 - 252 | 5 | X-RAY DIFFRACTION | 5 | A253 - 308 | 6 | X-RAY DIFFRACTION | 6 | A309 - 357 | 7 | X-RAY DIFFRACTION | 7 | A358 - 404 | 8 | X-RAY DIFFRACTION | 8 | A405 - 461 | 9 | X-RAY DIFFRACTION | 9 | A462 - 505 | 10 | X-RAY DIFFRACTION | 10 | A506 - 618 | | | | | | | | | | |
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