ソフトウェア | 名称 | バージョン | 分類 |
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Blu-Ice | | データ収集 | XDS | | データ削減 | XSCALE | | データスケーリング | PHASER | | 位相決定 | Coot | | モデル構築 | PHENIX | (phenix.refine: 1.9_1692)精密化 | PDB_EXTRACT | 3.15 | データ抽出 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.5→45.929 Å / SU ML: 0.18 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 25.18 / 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 | 0.2091 | 1817 | 3.88 % | RANDOM |
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Rwork | 0.1793 | 45067 | - | - |
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obs | 0.1805 | 46884 | 91.32 % | - |
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溶媒の処理 | 減衰半径: 0.5 Å / VDWプローブ半径: 0.9 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso max: 210.29 Å2 / Biso mean: 47.768 Å2 / Biso min: 18.79 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.5→45.929 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2703 | 0 | 55 | 162 | 2920 |
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Biso mean | - | - | 72.65 | 49.43 | - |
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残基数 | - | - | - | - | 352 |
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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_d0.004 | 3019 | X-RAY DIFFRACTION | f_angle_d0.698 | 4086 | X-RAY DIFFRACTION | f_chiral_restr0.028 | 468 | X-RAY DIFFRACTION | f_plane_restr0.002 | 566 | X-RAY DIFFRACTION | f_dihedral_angle_d12.601 | 1224 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.5-1.5406 | 0.4569 | 113 | 0.3588 | 2828 | 2941 | 76 | 1.5406-1.5859 | 0.3698 | 114 | 0.333 | 2944 | 3058 | 78 | 1.5859-1.6371 | 0.3096 | 123 | 0.2961 | 3095 | 3218 | 82 | 1.6371-1.6956 | 0.3104 | 121 | 0.2686 | 3185 | 3306 | 85 | 1.6956-1.7635 | 0.3153 | 137 | 0.2481 | 3297 | 3434 | 88 | 1.7635-1.8438 | 0.2293 | 143 | 0.2167 | 3430 | 3573 | 91 | 1.8438-1.941 | 0.1979 | 137 | 0.2014 | 3533 | 3670 | 94 | 1.941-2.0626 | 0.2188 | 154 | 0.1775 | 3703 | 3857 | 98 | 2.0626-2.2219 | 0.1831 | 153 | 0.1565 | 3756 | 3909 | 99 | 2.2219-2.4455 | 0.1652 | 153 | 0.149 | 3775 | 3928 | 100 | 2.4455-2.7993 | 0.1935 | 154 | 0.1573 | 3799 | 3953 | 99 | 2.7993-3.5266 | 0.1847 | 158 | 0.1712 | 3850 | 4008 | 100 | 3.5266-45.9504 | 0.2144 | 157 | 0.1714 | 3872 | 4029 | 96 |
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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 | 0.2913 | -0.0099 | -0.0512 | 0.2039 | 0.0824 | 0.0909 | 0.0867 | 0.0725 | 0.0539 | -0.2591 | 0.5686 | 0.7542 | 0.045 | -0.9378 | -0.0005 | 0.3537 | -0.028 | -0.0505 | 0.6089 | 0.0814 | 0.5007 | -16.6002 | 12.7061 | -21.7028 | 2 | 0.5856 | -0.1022 | 0.6456 | 2.0188 | -0.3515 | 1.1062 | 0.0559 | 0.0704 | -0.0464 | -0.2064 | -0.0854 | -0.1089 | 0.0439 | -0.0558 | 0 | 0.2235 | 0.0261 | 0.0107 | 0.2333 | 0.0058 | 0.2263 | -7.3369 | 18.4977 | -15.159 | 3 | 0.6194 | -0.5821 | 0.5415 | 1.8192 | 0.5783 | 1.5176 | 0.0653 | 0.0106 | 0.0139 | 0.0432 | -0.1106 | -0.2986 | -0.0357 | 0.104 | 0 | 0.1945 | -0.0056 | -0.0003 | 0.2311 | 0.0226 | 0.2248 | -1.3564 | 27.6251 | -4.6919 | 4 | 0.6085 | -0.8802 | -0.2732 | 1.573 | -0.0972 | 1.0182 | 0.1506 | 0.2796 | 0.2559 | 0.105 | -0.3253 | -1.1471 | -0.1365 | 0.9617 | -0.0315 | 0.344 | -0.0658 | -0.0586 | 0.5053 | 0.0819 | 0.4933 | 6.6533 | 30.7538 | -1.7293 | 5 | 0.0777 | -0.1506 | -0.003 | 0.4743 | 0.4124 | 2.2173 | -0.1253 | 0.504 | 0.2461 | -0.4639 | 0.0312 | 0.4182 | 0.1436 | -0.8787 | -0.4596 | 0.397 | 0.0104 | -0.1436 | 0.5799 | 0.1372 | 0.3214 | -36.0557 | 26.642 | -22.127 | 6 | 1.3007 | 0.2179 | 0.3854 | 0.65 | -0.8348 | 1.7346 | 0.0794 | 0.5636 | -0.1467 | -1.22 | 0.0848 | -0.5132 | 0.3781 | -0.1876 | 0.77 | 0.6252 | 0.0871 | 0.1862 | 0.4528 | 0.0389 | 0.3489 | -25.9751 | 25.3873 | -21.278 | 7 | 0.3398 | -0.321 | -0.1105 | 0.8921 | 0.565 | 0.3663 | 0.1107 | 0.365 | 0.2378 | -0.3177 | 0.3873 | 0.3229 | -0.4184 | -0.864 | 0.0093 | 0.3241 | 0.059 | 0.0335 | 0.353 | 0.0992 | 0.2446 | -32.5593 | 32.9566 | -14.9317 | 8 | 0.6825 | -0.348 | -0.0092 | 1.6481 | 0.6533 | 1.8291 | 0.0488 | 0.1106 | 0.1681 | -0.2799 | 0.0077 | -0.4267 | -0.281 | 0.2742 | 0.0003 | 0.2603 | 0.0111 | 0.0604 | 0.2659 | 0.0436 | 0.3061 | -23.0276 | 33.8618 | -7.885 | 9 | 0.668 | -0.2212 | 0.3136 | 0.4676 | 0.3348 | 0.5693 | 0.1563 | 0.1299 | 0.1752 | 0.1309 | 0.0081 | 0.0558 | -0.7253 | -0.189 | 0.0001 | 0.4015 | 0.0192 | 0.0459 | 0.233 | 0.0203 | 0.3078 | -25.6568 | 43.1355 | 0.6632 | 10 | 0.3943 | 0.4333 | -0.0049 | 0.8567 | 0.3119 | 0.2752 | -0.2043 | -0.2178 | 0.1018 | 0.1801 | -0.0411 | -0.6672 | -0.1218 | 0.4974 | -0.0119 | 0.2769 | -0.0574 | -0.0088 | 0.3582 | 0.0283 | 0.4536 | -15.5039 | 39.4219 | 3.826 |
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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 2:22 )A2 - 22 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 23:109 )A23 - 109 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 110:154 )A110 - 154 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN A AND RESID 155:178 )A155 - 178 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN B AND RESID 2:23 )B2 - 23 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN B AND RESID 24:45 )B24 - 45 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN B AND RESID 46:66 )B46 - 66 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN B AND RESID 67:131 )B67 - 131 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN B AND RESID 132:154 )B132 - 154 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN B AND RESID 155:176 )B155 - 176 | | | | | | | | | | | | | | | | | | | | |
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