ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データ収集 | PHASER | | 位相決定 | REFMAC | 5.2.0005精密化 | HKL-2000 | | データ削減 | HKL-2000 | | 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 1W4X 解像度: 2.3→26.53 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.129 / SU ML: 0.178 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.255 / 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 | 0.24514 | 2613 | 10 % | RANDOM |
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Rwork | 0.18267 | - | - | - |
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obs | 0.18889 | 23460 | 99.88 % | - |
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all | - | 23488 | - | - |
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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: 44.075 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.9 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.7 Å2 | 0 Å2 |
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3- | - | - | -0.2 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.3→26.53 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4173 | 0 | 127 | 149 | 4449 |
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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 | 4427 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.473 | 1.973 | 6056 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.63 | 5 | 532 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg35.783 | 23.726 | 212 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg17.081 | 15 | 653 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.13 | 15 | 30 | X-RAY DIFFRACTION | r_chiral_restr0.106 | 0.2 | 649 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 3436 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined0.201 | 0.2 | 2110 | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined0.309 | 0.2 | 2988 | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.16 | 0.2 | 256 | 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_refined0.163 | 0.2 | 29 | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.168 | 0.2 | 8 | 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_it0.547 | 1.5 | 2701 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it0.924 | 2 | 4249 | X-RAY DIFFRACTION | r_scbond_it1.495 | 3 | 2070 | X-RAY DIFFRACTION | r_scangle_it2.312 | 4.5 | 1806 | 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: 2.3→2.424 Å / Total num. of bins used: 10
| Rfactor | 反射数 | %反射 |
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Rfree | 0.291 | 349 | - |
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Rwork | 0.209 | 3390 | - |
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obs | - | - | 99.97 % |
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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 | 1.9126 | -0.1731 | -0.0437 | 1.9638 | -0.1647 | 1.1135 | 0.0806 | 0.1327 | 0.07 | -0.2532 | 0.0528 | -0.1678 | 0.0286 | 0.0133 | -0.1335 | -0.1525 | -0.025 | -0.008 | -0.1298 | 0.0508 | -0.2293 | -11.8088 | 10.8352 | 0.2114 | 2 | 0.5841 | -2.4236 | 0.3885 | 10.0572 | -1.6123 | 0.2585 | -0.809 | -0.0356 | 0.0652 | 0.3827 | 0.5589 | -0.2174 | -0.3799 | 0.0852 | 0.2501 | 0.0239 | 0.0102 | -0.0929 | -0.0057 | 0.0652 | -0.1414 | -7.6421 | 0.4673 | 17.4909 | 3 | 0.7313 | -1.0999 | 0.7644 | 3.5231 | -0.9978 | 2.8116 | 0.0343 | -0.0774 | -0.1437 | -0.1153 | -0.0567 | -0.4008 | 0.1979 | 0.3561 | 0.0225 | -0.0532 | 0.0042 | -0.0605 | -0.0785 | 0.0637 | -0.0225 | -0.5186 | -12.5982 | 13.5646 | 4 | 3.3031 | -0.1688 | 1.2448 | 3.1666 | -1.8912 | 2.1686 | -0.0727 | 0.6281 | -0.357 | -0.7695 | 0.1759 | 0.3181 | 0.5138 | -0.2445 | -0.1032 | 0.168 | -0.1426 | -0.1787 | 0.0972 | 0.0041 | 0.006 | -25.8057 | -8.7553 | -4.9687 | 5 | 1.7276 | -1.0764 | 1.2225 | 1.8009 | -1.0263 | 1.6721 | 0.0787 | -0.2211 | -0.6134 | -0.2356 | 0.2567 | 0.4863 | 0.3656 | -0.1903 | -0.3353 | 0.0441 | -0.0685 | -0.0788 | -0.0299 | 0.1529 | 0.1377 | -17.5088 | -18.9309 | 15.4213 | 6 | 2.6411 | -0.0358 | 0.442 | 2.6362 | -0.0261 | 1.4049 | 0.0397 | -0.2659 | 0.1193 | 0.1954 | 0.0167 | 0.233 | 0.0409 | -0.1829 | -0.0564 | -0.1831 | -0.0425 | 0.0036 | -0.1139 | 0.049 | -0.2119 | -23.7161 | 14.2915 | 14.0318 | 7 | 9.9963 | 2.765 | 2.36 | 4.9929 | 1.6393 | 10.1821 | 0.1042 | -0.7921 | -0.2355 | 0.5684 | 0.5166 | 0.4775 | 0.584 | -0.3638 | -0.6208 | 0.0307 | -0.0198 | -0.033 | -0.041 | 0.1162 | -0.1186 | -19.3026 | -2.3737 | 23.2036 | 8 | 3.3138 | -2.5781 | 0.8047 | 6.1237 | -2.1737 | 3.1445 | 0.0907 | -0.1803 | 0.2036 | -0.0036 | 0.0842 | 0.4466 | -0.0051 | -0.4405 | -0.1749 | -0.2558 | -0.0246 | -0.0034 | -0.0904 | 0.1063 | -0.1353 | -31.7749 | 13.0779 | 10.234 | 9 | 16.7979 | 5.2742 | 3.7891 | 6.6012 | 2.0654 | 4.16 | -0.3817 | -0.2311 | -0.0914 | -0.9162 | 0.2728 | 0.0339 | -0.0289 | 0.1222 | 0.1088 | 0.0208 | -0.035 | -0.0475 | 0.0267 | 0.0201 | -0.0479 | -12.7284 | 3.2474 | 6.6678 | 10 | 3.6684 | -3.5338 | -1.6885 | 6.4069 | 1.0824 | 2.2402 | -0.3521 | -0.1539 | -0.4365 | -0.5177 | 1.1618 | 0.5048 | -0.091 | -0.7887 | -0.8098 | 0.0937 | -0.0722 | -0.0983 | 0.1193 | 0.0984 | 0.0778 | -12.4734 | -7.8043 | 16.2294 |
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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 | A6 - 142 | 2 | X-RAY DIFFRACTION | 2 | A143 - 154 | 3 | X-RAY DIFFRACTION | 3 | A155 - 211 | 4 | X-RAY DIFFRACTION | 4 | A212 - 251 | 5 | X-RAY DIFFRACTION | 5 | A252 - 385 | 6 | X-RAY DIFFRACTION | 6 | A386 - 486 | 7 | X-RAY DIFFRACTION | 7 | A487 - 502 | 8 | X-RAY DIFFRACTION | 8 | A503 - 535 | 9 | X-RAY DIFFRACTION | 9 | A541 | 10 | X-RAY DIFFRACTION | 10 | A542 | | | | | | | | | | |
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