ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.7.3_928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: 4P97 解像度: 2.59→19.403 Å / SU ML: 0.35 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 33.86 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2444 | 500 | 10.03 % |
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Rwork | 0.1925 | - | - |
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obs | 0.1979 | 4985 | 83.82 % |
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溶媒の処理 | 減衰半径: 0.98 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 91.673 Å2 / ksol: 0.298 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -21.4768 Å2 | 0 Å2 | -0 Å2 |
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2- | - | -21.4768 Å2 | 0 Å2 |
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3- | - | - | -52.3477 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.59→19.403 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 1136 | 1 | 0 | 1137 |
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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_d0.002 | 1266 | X-RAY DIFFRACTION | f_angle_d0.445 | 1966 | X-RAY DIFFRACTION | f_dihedral_angle_d14.08 | 632 | X-RAY DIFFRACTION | f_chiral_restr0.051 | 266 | X-RAY DIFFRACTION | f_plane_restr0.002 | 54 | | | | | |
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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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2.5963-2.8568 | 0.4811 | 53 | 0.4279 | 474 | X-RAY DIFFRACTION | 36 | 2.8568-3.2685 | 0.4152 | 141 | 0.3209 | 1271 | X-RAY DIFFRACTION | 98 | 3.2685-4.1116 | 0.2621 | 148 | 0.2473 | 1338 | X-RAY DIFFRACTION | 100 | 4.1116-19.4032 | 0.1986 | 158 | 0.1418 | 1402 | X-RAY DIFFRACTION | 100 |
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精密化 TLS | 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 | 0.4743 | -0.4892 | 0.6273 | 0.575 | -0.6049 | 0.8175 | -0.069 | 0.5182 | 0.1884 | -0.757 | -0.4073 | -0.596 | 1.1167 | 0.5105 | 0.0012 | 0.7332 | 0.0774 | 0.0538 | 0.7677 | -0.179 | 0.8781 | 48.034 | 19.191 | 314.9542 | 2 | 0.1278 | -0.2031 | 0.0486 | 0.4545 | 0.0982 | 0.2167 | -0.2147 | 0.8948 | -0.1075 | -0.1113 | 0.1664 | -0.6507 | -0.1178 | -0.6949 | 0.001 | 0.7613 | -0.0074 | -0.0208 | 0.589 | -0.0286 | 0.7115 | 45.9397 | 1.1546 | 319.9836 | 3 | 0.2425 | 0.0993 | 0.2936 | 0.0589 | 0.1816 | 0.486 | -0.6757 | 0.1955 | 0.5104 | -0.2893 | 0.2143 | -0.1226 | 0.1176 | -0.1109 | 0.0006 | 0.717 | -0.0497 | 0.1197 | 0.5672 | -0.1061 | 0.8007 | 51.1097 | 13.715 | 315.601 | 4 | 0.5954 | -0.2439 | 0.3916 | 0.9703 | -0.695 | 0.5783 | 0.0348 | 0.952 | -1.113 | -0.3558 | 0.8787 | -0.0619 | 0.5339 | 0.4162 | 0.0137 | 0.6469 | -0.0321 | -0.0424 | 0.9556 | -0.0553 | 1.078 | 69.5436 | 19.8698 | 319.0855 | 5 | 5.4197 | -0.6789 | 0.2031 | 0.7599 | 0.4293 | 0.3298 | -0.4373 | -0.9263 | 0.0995 | 1.4756 | 0.4195 | -0.5035 | 1.3481 | 0.1397 | 0.6066 | 1.7978 | -0.0785 | -0.4449 | 2.0205 | 0.2452 | 0.7158 | 70.3314 | -10.4381 | 357.8871 | 6 | 0.0046 | -0.0202 | 0.0047 | 0.0691 | -0.0184 | 0.0068 | -0.0899 | -0.2028 | 0.5001 | 0.8389 | 0.7471 | -1.0786 | -0.692 | 0.3415 | 0.006 | 1.0374 | 0.0893 | -0.2018 | 1.4578 | -0.1877 | 0.7214 | 78.525 | -24.8887 | 367.4228 | 7 | 3.7834 | -1.0847 | -1.6789 | 0.3501 | 0.4915 | 0.7462 | -0.941 | -0.472 | 0.0443 | -0.5019 | 0.0801 | -0.1131 | 0.3305 | 0.4012 | -1.5226 | 1.3951 | 0.1623 | -0.4007 | 1.995 | 0.0297 | 0.6296 | 75.3178 | -10.7416 | 359.4929 | 8 | 0.075 | -0.3101 | -0.0932 | 1.5418 | 0.5262 | 0.1853 | 0.1724 | -0.2893 | -0.9052 | 1.7091 | 0.4424 | -0.1736 | 0.7103 | 0.582 | 0.7082 | 1.5402 | -0.2033 | -0.0188 | 1.847 | 0.5361 | 0.9612 | 87.2368 | 4.6765 | 362.7994 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resseq 3:11)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 12:18)3 | X-RAY DIFFRACTION | 3 | chain 'B' and (resseq 37:42)4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resseq 43:47)5 | X-RAY DIFFRACTION | 5 | chain 'E' and (resseq 3:13)6 | X-RAY DIFFRACTION | 6 | chain 'E' and (resseq 14:18)7 | X-RAY DIFFRACTION | 7 | chain 'F' and (resseq 37:42)8 | X-RAY DIFFRACTION | 8 | chain 'F' and (resseq 43:47) | | | | | | | |
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