ソフトウェア | 名称 | バージョン | 分類 |
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HKL-2000 | | データスケーリング | PHENIX | 1.11.1_2575精密化 | PDB_EXTRACT | 3.24 | データ抽出 | HKL-2000 | | データ削減 | AutoSol | | 位相決定 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.405→49.308 Å / SU ML: 0.26 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 25.36
| Rfactor | 反射数 | %反射 |
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Rfree | 0.233 | 615 | 4.86 % |
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Rwork | 0.212 | - | - |
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obs | 0.213 | 12643 | 99.85 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å |
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原子変位パラメータ | Biso max: 147.07 Å2 / Biso mean: 61.7128 Å2 / Biso min: 33.44 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.405→49.308 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1938 | 0 | 0 | 2 | 1940 |
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Biso mean | - | - | - | 55.88 | - |
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残基数 | - | - | - | - | 228 |
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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 | 1976 | X-RAY DIFFRACTION | f_angle_d0.376 | 2646 | X-RAY DIFFRACTION | f_chiral_restr0.032 | 286 | X-RAY DIFFRACTION | f_plane_restr0.002 | 328 | X-RAY DIFFRACTION | f_dihedral_angle_d1.998 | 1194 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.4051-2.6471 | 0.2597 | 148 | 0.2478 | 2945 | 3093 | 99 | 2.6471-3.0301 | 0.2585 | 150 | 0.2256 | 3043 | 3193 | 100 | 3.0301-3.8174 | 0.2407 | 162 | 0.2154 | 2969 | 3131 | 100 | 3.8174-49.3188 | 0.2161 | 155 | 0.2003 | 3071 | 3226 | 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 | 8.5184 | 0.7662 | 2.5268 | 2.0756 | -2.0148 | 9.0725 | -0.6808 | 0.1844 | -0.5093 | -0.2931 | 0.389 | -1.1392 | -0.073 | 1.1264 | 0.1674 | 0.3982 | -0.093 | 0.0087 | 0.865 | 0.06 | 0.6507 | 47.335 | 28.017 | 7.612 | 2 | 5.0197 | -1.392 | -1.1165 | 7.398 | 1.8792 | 7.8384 | 0.0481 | -0.0879 | 0.1924 | 0.336 | 0.2563 | 0.5154 | 0.3344 | -0.7856 | -0.2648 | 0.4119 | 0.0479 | 0.001 | 0.5122 | 0.0801 | 0.5472 | 31.828 | 31.629 | 2.222 | 3 | 7.4373 | 0.4249 | -1.7898 | 6.5015 | -0.2839 | 2.0517 | 0.3412 | 0.9624 | -1.7429 | -0.7843 | -0.0328 | -0.1517 | 2.2262 | 0.3016 | -0.4199 | 0.929 | 0.0367 | -0.1901 | 0.8549 | -0.2641 | 0.9954 | 32.799 | 17.332 | -15.276 | 4 | 9.0715 | -0.9421 | -0.6325 | 2.0873 | 0.9205 | 9.7892 | 0.2964 | 1.0269 | -0.3842 | -0.9911 | 0.3259 | 0.8899 | 0.4527 | -0.6974 | -0.6233 | 0.5706 | -0.0224 | -0.0809 | 0.5076 | 0.0911 | 0.5388 | 31.691 | 31.455 | -12.689 | 5 | 6.2547 | -1.9446 | 2.1485 | 2.7799 | -1.4843 | 3.6007 | -0.2191 | -0.0125 | -0.1266 | 0.2275 | 0.3173 | 0.214 | -0.2682 | -0.2679 | -0.0861 | 0.4143 | -0.0042 | 0.0103 | 0.4054 | 0.0652 | 0.4431 | 37.262 | 37.573 | -2.448 | 6 | 6.1241 | 0.7412 | 2.5077 | 3.2034 | 0.3519 | 8.5145 | 0.1657 | 0.4108 | -0.7993 | -0.2299 | 0.1318 | 0.1735 | 1.0118 | 0.4654 | -0.2777 | 0.3685 | 0.0206 | -0.0509 | 0.2941 | -0.0039 | 0.5085 | 39.75 | 24.497 | -3.991 | 7 | 4.6794 | 0.3235 | -0.0491 | 4.3097 | -0.2518 | 3.103 | 0.0195 | -0.0197 | 0.259 | 0.045 | 0.1163 | 0.0286 | -0.2662 | -0.1491 | -0.0607 | 0.4537 | -0.0349 | -0.0081 | 0.5639 | -0.0425 | 0.4098 | 20.138 | 13.687 | 12.834 | 8 | 2.7572 | -0.4582 | 4.5827 | 5.6201 | 0.7953 | 8.0559 | 0.1676 | -0.0305 | -1.7318 | 0.2852 | 0.203 | -0.7028 | 1.1794 | 1.1191 | -0.2464 | 0.9106 | 0.2189 | 0.1065 | 0.7145 | -0.06 | 0.8981 | 39.776 | 0.767 | 8.01 | 9 | 9.0893 | -0.9252 | -0.3081 | 2.1673 | 0.8044 | 9.845 | -0.627 | 0.525 | -0.2191 | -0.9943 | 0.381 | -1.2863 | 0.5626 | 1.0889 | 0.3048 | 0.5332 | -0.1154 | 0.0988 | 0.5372 | 0.0477 | 0.5322 | 36.946 | 15.455 | 7.526 | 10 | 3.2088 | 0.911 | -1.8478 | 4.1158 | -4.2468 | 7.508 | 0.0455 | 0.1701 | -0.0464 | 0.1434 | 0.1133 | 0.3347 | 0.1721 | 0.0467 | -0.0781 | 0.3872 | -0.0778 | -0.0054 | 0.3539 | 0.0169 | 0.39 | 25.92 | 20.92 | 12.243 | 11 | 8.6369 | -1.5668 | -1.5868 | 8.5986 | 2.7683 | 7.0402 | -0.229 | -0.995 | -1.0804 | -0.2286 | 0.1716 | -0.6674 | 1.0402 | 1.3707 | 0.0448 | 0.5502 | 0.142 | 0.0761 | 0.6698 | 0.0153 | 0.5251 | 37.135 | 7.596 | 16.928 | 12 | 1.2527 | 0.3119 | -0.9651 | 3.9371 | 0.3723 | 5.9137 | -0.1398 | 0.7302 | -1.0128 | -0.3068 | 0.0117 | -0.1855 | 0.6228 | -0.4507 | 0.1727 | 0.488 | -0.0698 | 0.02 | 0.3621 | -0.0249 | 0.3605 | 19.831 | 8.821 | 13.463 |
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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 1:12 )A1 - 12 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN A AND RESID 13:45 )A13 - 45 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN A AND RESID 46:62 )A46 - 62 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN A AND RESID 63:72 )A63 - 72 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN A AND RESID 73:93 )A73 - 93 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN A AND RESID 94:125 )A94 - 125 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN B AND RESID 1:44 )B1 - 44 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN B AND RESID 45:62 )B45 - 62 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN B AND RESID 63:73 )B63 - 73 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN B AND ( RESID 74:90 OR RESID 91:91 ) )B74 - 90 | 11 | X-RAY DIFFRACTION | 10 | ( CHAIN B AND ( RESID 74:90 OR RESID 91:91 ) )B91 | 12 | X-RAY DIFFRACTION | 11 | ( CHAIN B AND RESID 92:109 )B92 - 109 | 13 | X-RAY DIFFRACTION | 12 | ( CHAIN B AND RESID 110:125 )B110 - 125 | | | | | | | | | | | | | | | | | | | | | | | | | | |
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