ソフトウェア | 名称 | バージョン | 分類 | NB |
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PHENIX | 1.7.3_928精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | PHENIX | | 位相決定 | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.7→49.32 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.31 / σ(F): 1.35 / 位相誤差: 20.74 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.218 | 1260 | 10.04 % |
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Rwork | 0.17 | - | - |
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obs | 0.175 | 12544 | 100 % |
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all | - | 13804 | - |
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溶媒の処理 | 減衰半径: 0.73 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 48.45 Å2 / ksol: 0.4 e/Å3 |
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原子変位パラメータ | Biso mean: 53.49 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0 Å2 | -0 Å2 | -0 Å2 |
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2- | - | 0 Å2 | -0 Å2 |
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3- | - | - | 0 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.7→49.32 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2163 | 0 | 10 | 55 | 2228 |
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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_d0.008 | 2226 | X-RAY DIFFRACTION | f_angle_d1.117 | 3004 | X-RAY DIFFRACTION | f_dihedral_angle_d13.597 | 820 | X-RAY DIFFRACTION | f_chiral_restr0.061 | 323 | X-RAY DIFFRACTION | f_plane_restr0.007 | 388 | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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2.7011-2.8093 | 0.3078 | 138 | 0.2427 | 1232 | X-RAY DIFFRACTION | 100 | 2.8093-2.9371 | 0.2757 | 135 | 0.2246 | 1254 | X-RAY DIFFRACTION | 100 | 2.9371-3.0919 | 0.2659 | 134 | 0.1917 | 1232 | X-RAY DIFFRACTION | 100 | 3.0919-3.2856 | 0.2868 | 138 | 0.1917 | 1229 | X-RAY DIFFRACTION | 100 | 3.2856-3.5392 | 0.2511 | 145 | 0.1759 | 1252 | X-RAY DIFFRACTION | 100 | 3.5392-3.8953 | 0.1995 | 135 | 0.1498 | 1244 | X-RAY DIFFRACTION | 100 | 3.8953-4.4586 | 0.151 | 140 | 0.1263 | 1259 | X-RAY DIFFRACTION | 100 | 4.4586-5.6161 | 0.1887 | 143 | 0.138 | 1271 | X-RAY DIFFRACTION | 100 | 5.6161-49.3287 | 0.2098 | 152 | 0.1958 | 1311 | X-RAY DIFFRACTION | 100 |
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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 | 5.4474 | -0.7544 | 1.0778 | 1.0221 | 1.8075 | 4.8344 | -0.1517 | 0.2673 | -0.1752 | -0.4614 | 0.048 | 0.2192 | -0.1691 | -0.2447 | 0.0804 | 0.304 | -0.061 | -0.1492 | 0.2045 | 0.01 | 0.3025 | 85.755 | 62.205 | 78.188 | 2 | 3.8242 | -5.4663 | -0.5282 | 9.6047 | 3.9256 | 5.9948 | -0.1382 | 0.1962 | 0.2461 | -0.3767 | -0.2888 | 0.1243 | -0.3163 | -0.1543 | 0.2469 | 0.5473 | -0.2355 | -0.0794 | 0.3798 | -0.0714 | 0.624 | 89.629 | 57.275 | 97.342 | 3 | 4.0916 | 0.4987 | 0.2788 | 1.4478 | 0.6034 | 2.5826 | -0.0065 | 0.4175 | -0.3134 | -0.5084 | -0.0063 | 0.202 | 0.2806 | -0.2626 | 0.0078 | 0.32 | -0.0706 | -0.1018 | 0.1858 | -0.0497 | 0.2397 | 89.624 | 64.729 | 83.184 | 4 | 2.3872 | -0.3299 | 0.3453 | 1.3035 | -0.0609 | 1.8745 | 0.1442 | 0.0671 | 0.0285 | -0.2734 | 0.0368 | 0.5373 | -0.1759 | -0.3824 | -0.1654 | 0.2537 | 0.0113 | -0.1509 | 0.2315 | 0.0741 | 0.3777 | 81.087 | 50.348 | 65.009 | 5 | 1.8849 | 0.1576 | 0.5973 | 0.7913 | 0.1301 | 1.5797 | -0.0424 | 0.033 | 0.2047 | -0.1306 | -0.0147 | 0.4491 | -0.1825 | -0.4034 | -0.0745 | 0.1072 | 0.0757 | -0.0627 | 0.1758 | 0.0337 | 0.2692 | 74.078 | 49.63 | 64.794 |
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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 2:41 )A2 - 41 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 42:67 )A42 - 67 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 68:141 )A68 - 141 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN B AND RESID 2:78 )B2 - 78 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN B AND RESID 79:139 )B79 - 139 | | | | | | | | | | |
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