ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALEPACK | | データスケーリング | | PHENIX | 1.6.1_357精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | MAR345dtb | | データ収集 | | HKL-2000 | | データ削減 | | CNS | | 位相決定 | | |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: PDB entry 3OGZ 解像度: 2.14→29.517 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8497 / SU ML: 0.24 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 1.33 / σ(I): 0 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2034 | 2113 | 5.06 % | RANDOM |
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Rwork | 0.1679 | - | - | - |
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obs | 0.1697 | 41728 | 98.72 % | - |
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all | - | 41728 | - | - |
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溶媒の処理 | 減衰半径: 0.8 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 65.751 Å2 / ksol: 0.357 e/Å3 |
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原子変位パラメータ | Biso max: 188.3 Å2 / Biso mean: 60.9787 Å2 / Biso min: 24.5 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 12.5713 Å2 | -0 Å2 | -9.0136 Å2 |
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2- | - | -10.9628 Å2 | -0 Å2 |
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3- | - | - | -1.6085 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.25 Å | 0.24 Å |
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Luzzati d res low | - | 8 Å |
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Luzzati sigma a | 0.27 Å | 0.23 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.14→29.517 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4504 | 0 | 42 | 253 | 4799 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.01 | 4676 | X-RAY DIFFRACTION | f_angle_d1.271 | 6361 | X-RAY DIFFRACTION | f_chiral_restr0.083 | 730 | X-RAY DIFFRACTION | f_plane_restr0.005 | 822 | X-RAY DIFFRACTION | f_dihedral_angle_d17.715 | 1763 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.14-2.1824 | 0.2429 | 124 | 0.1974 | 2538 | 2662 | 95 | 2.1824-2.2369 | 0.2268 | 133 | 0.1867 | 2657 | 2790 | 100 | 2.2369-2.2974 | 0.2253 | 149 | 0.1835 | 2683 | 2832 | 100 | 2.2974-2.365 | 0.2554 | 135 | 0.18 | 2644 | 2779 | 100 | 2.365-2.4413 | 0.2258 | 139 | 0.178 | 2707 | 2846 | 100 | 2.4413-2.5285 | 0.2071 | 136 | 0.1733 | 2639 | 2775 | 100 | 2.5285-2.6296 | 0.2626 | 159 | 0.1912 | 2675 | 2834 | 100 | 2.6296-2.7492 | 0.2582 | 155 | 0.1984 | 2633 | 2788 | 100 | 2.7492-2.8941 | 0.2501 | 149 | 0.2003 | 2694 | 2843 | 100 | 2.8941-3.0752 | 0.2332 | 149 | 0.1898 | 2655 | 2804 | 100 | 3.0752-3.3124 | 0.2121 | 126 | 0.1849 | 2668 | 2794 | 100 | 3.3124-3.6451 | 0.2137 | 156 | 0.1632 | 2653 | 2809 | 99 | 3.6451-4.1713 | 0.1725 | 153 | 0.1459 | 2639 | 2792 | 99 | 4.1713-5.2506 | 0.1418 | 136 | 0.1264 | 2622 | 2758 | 97 | 5.2506-29.5199 | 0.1784 | 114 | 0.1593 | 2508 | 2622 | 91 |
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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 | 2.5035 | 0.3637 | -1.0217 | 0.6936 | 0.171 | 1.1817 | 0.079 | -0.0865 | 0.2475 | 0.2446 | -0.0127 | 0.1539 | 0.5279 | -0.3414 | -0.062 | 0.5489 | -0.2843 | 0.066 | 0.6752 | -0.1138 | 0.6206 | 7.0736 | 29.9821 | 47.9936 | 2 | 1.9649 | 1.5483 | -0.2349 | 3.155 | 0.0953 | 0.0615 | 0.2879 | -0.0243 | 0.5887 | -0.4163 | 0.0071 | -1.0891 | -0.8009 | 0.7895 | -0.2521 | 0.6737 | -0.3716 | 0.0674 | 0.7539 | -0.009 | 0.9266 | 29.7383 | 13.0637 | 24.8191 | 3 | 1.4131 | -0.0721 | 0.3957 | 1.8841 | 0.3782 | 2.4112 | 0.1589 | -0.0781 | 0.002 | 0.0491 | -0.1504 | -0.2278 | -0.0715 | 0.0726 | -0.0068 | 0.1715 | -0.0706 | 0.0257 | 0.2749 | 0.0576 | 0.1975 | 9.4399 | -6.6592 | 24.96 | 4 | 0.5526 | -0.1615 | 0.4329 | 0.1834 | 0.0833 | 0.658 | -0.053 | 0.2392 | -0.1085 | -0.2119 | -0.0402 | 0.2811 | -0.2349 | 0.1184 | 0.0675 | 0.7052 | -0.1705 | -0.1373 | 0.5013 | -0.0174 | 0.5717 | 14.3436 | 25.8103 | 30.1066 | 5 | 2.0373 | 1.6272 | 0.1304 | 1.5873 | 0.5638 | 0.709 | 0.0911 | 0.1495 | 0.5944 | -0.192 | -0.273 | 0.5524 | 0.1142 | -0.4196 | 0.209 | 0.5182 | -0.1713 | -0.0858 | 0.5836 | -0.0964 | 0.7198 | 5.175 | 25.7169 | 37.7943 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | chain A and (resid 1:76)A1 - 76 | 2 | X-RAY DIFFRACTION | 2 | chain A and (resid 77:85 or resid 300:356)A77 - 85 | 3 | X-RAY DIFFRACTION | 2 | chain A and (resid 77:85 or resid 300:356)A300 - 356 | 4 | X-RAY DIFFRACTION | 3 | chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A86 - 195 | 5 | X-RAY DIFFRACTION | 3 | chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A224 - 299 | 6 | X-RAY DIFFRACTION | 3 | chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A357 - 378 | 7 | X-RAY DIFFRACTION | 3 | chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A406 - 615 | 8 | X-RAY DIFFRACTION | 4 | chain A and (resid 379:405)A | | | | | | | | | | | | | | | |
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