ソフトウェア | 名称 | バージョン | 分類 |
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XDS | | データ削減 | XSCALE | | データスケーリング | PHENIX | 1.19rc4-4035 | 精密化 | PDB_EXTRACT | 3.27 | データ抽出 | MoRDa | | 位相決定 |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 3ts7 解像度: 1.85→29.67 Å / SU ML: 0.17 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 18.38 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1879 | 2033 | 4.56 % |
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Rwork | 0.1513 | 42504 | - |
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obs | 0.153 | 44537 | 98.75 % |
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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 / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso max: 81.02 Å2 / Biso mean: 25.4627 Å2 / Biso min: 8.86 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.85→29.67 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4074 | 0 | 13 | 457 | 4544 |
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Biso mean | - | - | 36.09 | 31.41 | - |
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残基数 | - | - | - | - | 553 |
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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: 15 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.85-1.89 | 0.2872 | 122 | 0.2182 | 2443 | 2565 | 87 | 1.89-1.94 | 0.2567 | 138 | 0.1826 | 2771 | 2909 | 97 | 1.94-1.99 | 0.2078 | 147 | 0.1701 | 2749 | 2896 | 98 | 1.99-2.05 | 0.218 | 146 | 0.1606 | 2794 | 2940 | 100 | 2.05-2.12 | 0.17 | 107 | 0.1421 | 2864 | 2971 | 100 | 2.12-2.19 | 0.2011 | 123 | 0.1383 | 2856 | 2979 | 100 | 2.19-2.28 | 0.1756 | 142 | 0.1441 | 2831 | 2973 | 100 | 2.28-2.38 | 0.1879 | 131 | 0.1445 | 2836 | 2967 | 100 | 2.38-2.51 | 0.1992 | 131 | 0.1546 | 2865 | 2996 | 100 | 2.51-2.67 | 0.2012 | 139 | 0.1627 | 2848 | 2987 | 100 | 2.67-2.87 | 0.2223 | 147 | 0.1543 | 2879 | 3026 | 100 | 2.87-3.16 | 0.2 | 145 | 0.1554 | 2857 | 3002 | 100 | 3.16-3.62 | 0.164 | 136 | 0.1476 | 2903 | 3039 | 100 | 3.62-4.56 | 0.1553 | 138 | 0.1263 | 2933 | 3071 | 100 | 4.56-29.67 | 0.1684 | 141 | 0.1598 | 3075 | 3216 | 99 |
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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 | 4.3408 | 1.7778 | -1.8221 | 4.3569 | -1.1489 | 3.3161 | -0.328 | 0.3105 | -0.3924 | -0.1991 | 0.1351 | 0.0383 | 0.5075 | -0.2459 | 0.2105 | 0.1885 | -0.0027 | 0.0016 | 0.1583 | -0.0686 | 0.1828 | -4.6028 | -6.5569 | -23.9171 | 2 | 4.8219 | 1.367 | -1.8037 | 2.6098 | -0.0763 | 1.8051 | -0.1134 | 0.3041 | -0.3376 | -0.1366 | 0.0313 | -0.1437 | 0.1593 | -0.0796 | 0.0227 | 0.1507 | 0.0196 | -0.0169 | 0.1024 | -0.0363 | 0.0959 | 1.6042 | 1.7319 | -24.2135 | 3 | 1.7214 | 0.2764 | -0.4172 | 1.2133 | 0.1384 | 1.0182 | -0.0384 | 0.0253 | -0.1437 | 0.0534 | 0.0071 | -0.18 | 0.0865 | 0.1235 | 0.0238 | 0.1209 | 0.0186 | -0.0069 | 0.0913 | -0.0048 | 0.1144 | 6.6133 | 9.0915 | -19.7575 | 4 | 1.4196 | 0.0561 | 0.2941 | 1.9033 | -0.3548 | 2.2882 | -0.0112 | -0.1258 | -0.0091 | 0.2691 | -0.0715 | -0.1922 | -0.1061 | 0.151 | 0.0964 | 0.1525 | -0.0018 | -0.0086 | 0.101 | -0.0004 | 0.1042 | 1.5084 | 10.2017 | -5.9239 | 5 | 3.0206 | -0.3651 | 1.2546 | 2.0265 | -0.3451 | 3.5675 | -0.0814 | -0.0719 | -0.3321 | 0.1132 | 0.127 | -0.1357 | 0.1659 | 0.1925 | -0.0122 | 0.1482 | 0.0151 | 0.035 | 0.1041 | -0.0056 | 0.1419 | -1.5534 | -1.021 | 0.5995 | 6 | 6.0993 | 0.2236 | 2.6706 | 3.0348 | 0.6167 | 5.7477 | 0.0037 | 0.086 | -0.6464 | 0.0434 | 0.0114 | -0.0114 | 0.4799 | 0.1672 | -0.108 | 0.2577 | -0.0192 | 0.0454 | 0.1218 | -0.0033 | 0.2445 | -10.1735 | -6.9593 | -8.078 | 7 | 1.6889 | -0.7667 | 0.6225 | 2.0976 | -1.2265 | 2.2616 | 0.0989 | 0.0172 | 0.1678 | -0.0284 | -0.0772 | -0.0251 | -0.2978 | -0.0563 | -0 | 0.1561 | 0.0093 | 0.0136 | 0.0924 | -0.0094 | 0.1117 | 5.9283 | 33.6618 | -19.2725 | 8 | 3.7959 | 0.5684 | 2.2209 | 0.9554 | 0.0539 | 2.5095 | -0.0213 | -0.0065 | 0.1215 | -0.0293 | -0.0242 | 0.0062 | -0.0968 | 0.0673 | 0.0397 | 0.1176 | 0.0086 | 0.0199 | 0.0612 | -0.0071 | 0.1037 | 9.568 | 23.0647 | -19.129 | 9 | 0.3527 | 0.8037 | -0.6295 | 2.8039 | -0.2794 | 2.8158 | 0.1989 | 0.2881 | -0.0568 | -0.4583 | -0.1955 | -0.463 | 0.0584 | 0.2432 | -0.0225 | 0.2066 | 0.0436 | 0.055 | 0.177 | 0.005 | 0.1476 | 12.0683 | 22.9393 | -34.6488 | 10 | 3.337 | 0.4892 | -0.56 | 4.3099 | -0.8876 | 4.0842 | -0.1089 | 0.1629 | -0.1262 | -0.2375 | -0.0813 | -0.7219 | -0.1269 | 0.4645 | 0.0344 | 0.2466 | 0.0651 | 0.0508 | 0.2544 | 0.0593 | 0.2141 | 15.8536 | 34.1119 | -40.4077 | 11 | 3.1366 | -0.4203 | -0.2741 | 4.9026 | -1.0559 | 4.5133 | 0.3177 | 0.2658 | 0.3048 | 0.3998 | 0.0102 | -0.0743 | -0.7323 | 0.0132 | -0.0661 | 0.4831 | 0.0748 | 0.0812 | 0.187 | 0.0609 | 0.1907 | 7.1203 | 42.8813 | -36.9634 |
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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 0 through 21 )A0 - 21 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 22 through 66 )A22 - 66 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 67 through 146 )A67 - 146 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 147 through 197 )A147 - 197 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 198 through 269 )A198 - 269 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 270 through 292 )A270 - 292 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 0 through 84 )B0 - 84 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 85 through 146 )B85 - 146 | 9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 147 through 197 )B147 - 197 | 10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 198 through 269 )B198 - 269 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 270 through 292 )B270 - 292 | | | | | | | | | | | | | | | | | | | | | | |
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