ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (PHENIX.REFINE)精密化 | MOSFLM | | データ削減 | SCALA | | データスケーリング | SHELX | | 位相決定 | |
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精密化 | 構造決定の手法: 多波長異常分散 開始モデル: NONE 解像度: 2.67→99.964 Å / SU ML: 0.42 / σ(F): 0 / 位相誤差: 22.04 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2403 | 694 | 5 % |
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Rwork | 0.1953 | - | - |
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obs | 0.1974 | 13832 | 96.89 % |
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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: 49.655 Å2 / ksol: 0.347 e/Å3 |
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原子変位パラメータ | Biso mean: 62.21 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: 2.67→99.964 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1906 | 0 | 10 | 45 | 1961 |
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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_d0.009 | 1964 | X-RAY DIFFRACTION | f_angle_d1.199 | 2652 | X-RAY DIFFRACTION | f_dihedral_angle_d14.413 | 690 | X-RAY DIFFRACTION | f_chiral_restr0.072 | 276 | X-RAY DIFFRACTION | f_plane_restr0.004 | 342 | | | | | |
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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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2.6702-2.8764 | 0.4016 | 141 | 0.3297 | 2354 | X-RAY DIFFRACTION | 90 | 2.8764-3.1659 | 0.3016 | 135 | 0.2437 | 2535 | X-RAY DIFFRACTION | 96 | 3.1659-3.624 | 0.2541 | 140 | 0.204 | 2639 | X-RAY DIFFRACTION | 98 | 3.624-4.5659 | 0.2162 | 151 | 0.1634 | 2697 | X-RAY DIFFRACTION | 100 | 4.5659-100.0338 | 0.1959 | 127 | 0.1797 | 2913 | 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 | 3.1357 | 1.108 | 1.7024 | 0.4032 | 0.6476 | 1.0295 | -0.873 | 0.3517 | 0.8649 | 0.5192 | 1.5999 | 0.98 | -0.3183 | 0.7726 | 0.3368 | 0.4818 | 0.0546 | 0.1211 | 0.3604 | 0.045 | 0.4935 | 65.3217 | 77.4556 | 57.4603 | 2 | 0.6 | 0.4392 | 0.2119 | 0.596 | -0.1941 | 0.1378 | 0.0202 | 0.4954 | -0.3189 | 0.0489 | -0.417 | 0.4155 | 0.0117 | -0.0766 | 0.0003 | 0.3778 | 0.0821 | -0.0183 | 0.3988 | 0.0288 | 0.3751 | 70.2901 | 65.3518 | 47.3817 | 3 | 0.6803 | -0.5969 | 0.1956 | 0.8654 | 0.1361 | 0.3359 | 0.0225 | 0.1373 | 0.4487 | -1.0577 | 0.1204 | -0.3245 | -0.5395 | -0.5808 | 0.0228 | 0.3533 | 0.0099 | 0.0084 | 0.383 | 0.0771 | 0.3637 | 77.8142 | 70.1979 | 40.8683 | 4 | 0.1009 | 0.0829 | 0.2386 | 0.2596 | 0.3433 | 0.2456 | 0.1255 | -0.0751 | 0.2415 | 0.0302 | -0.1199 | -0.4723 | -0.0452 | 0.3761 | 0.0001 | 0.3429 | 0.0138 | 0.0266 | 0.4033 | 0.092 | 0.481 | 76.1374 | 76.6898 | 49.1564 | 5 | 1.0734 | -0.7754 | -0.1613 | 0.4487 | 0.2049 | 0.1408 | -0.0451 | 0.0115 | -0.0009 | 0.1197 | -0.0091 | 0.0906 | 0.1913 | -0.0417 | 0.0003 | 0.3949 | -0.0015 | 0.0397 | 0.3512 | 0.0099 | 0.2648 | 74.0684 | 64.0505 | 52.0317 | 6 | 0.0686 | 0.0002 | 0.2126 | 0.0151 | 0.0041 | 0.3838 | -0.6721 | 0.1008 | -0.2614 | -0.1171 | 0.6408 | 0.2814 | 0.7619 | 1.4346 | 0.0152 | 0.4804 | 0.1644 | -0.0189 | 0.5568 | 0.0819 | 0.5215 | 86.5217 | 73.9543 | 66.7253 | 7 | 0.7158 | 0.203 | -0.3235 | 0.1802 | 0.2569 | 0.8207 | 0.018 | 0.0645 | 0.482 | 0.3763 | -0.0717 | 0.1164 | -0.3709 | 0.2304 | -0 | 0.3255 | -0.0341 | -0.0283 | 0.415 | -0.048 | 0.5357 | 84.7302 | 90.8761 | 68.1839 | 8 | 0.0972 | -0.0477 | -0.0631 | 0.0619 | 0.0187 | 0.068 | 0.2451 | -0.8257 | -0.5816 | 0.5036 | -0.5785 | -0.1093 | 0.704 | 0.0516 | -0.0007 | 0.5667 | -0.2058 | -0.1103 | 0.6836 | 0.0179 | 0.6458 | 91.455 | 89.5791 | 66.2623 | 9 | 0.2959 | -0.0059 | 0.1447 | 0.2398 | 0.329 | 0.6646 | 0.12 | 0.1711 | -0.0311 | -0.905 | 0.0534 | -0.2766 | -1.0284 | 1.4923 | -0.0432 | 0.4966 | -0.2575 | -0.0125 | 0.5657 | 0.119 | 0.6495 | 87.4304 | 93.9204 | 57.4921 | 10 | 1.3753 | 0.5793 | -0.9873 | 0.9245 | 0.8211 | 3.2467 | 0.5039 | -0.2697 | -0.214 | -0.9611 | 0.2429 | 0.9025 | -0.8453 | 0.5364 | 0.4409 | 0.3579 | -0.0484 | -0.04 | 0.5664 | 0.0597 | 0.7347 | 80.0271 | 89.1166 | 60.1502 | 11 | 0.2616 | 0.2518 | 0.2291 | 0.2155 | 0.1316 | 0.2194 | 0.54 | -0.3013 | 0.1227 | -0.4167 | -0.2728 | -0.1813 | -0.3405 | 0.3754 | 0.0004 | 0.477 | 0.0349 | 0.0049 | 0.5902 | -0.025 | 0.6057 | 87.9706 | 80.0115 | 55.3865 | 12 | 0.9102 | 0.7849 | 0.6023 | 1.9196 | 0.1819 | 0.5523 | -0.0021 | -0.0007 | 0.2005 | 0.1276 | -0.0402 | 1.0292 | -0.2882 | 0.0874 | 0.5997 | 0.5743 | -0.2018 | -0.0339 | 0.3416 | -0.0492 | 0.5108 | 79.987 | 89.6083 | 67.6573 |
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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 7:16)2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESSEQ 17:50)3 | X-RAY DIFFRACTION | 3 | CHAIN A AND (RESSEQ 51:67)4 | X-RAY DIFFRACTION | 4 | CHAIN A AND (RESSEQ 68:96)5 | X-RAY DIFFRACTION | 5 | CHAIN A AND (RESSEQ 97:129)6 | X-RAY DIFFRACTION | 6 | CHAIN B AND (RESSEQ 7:16)7 | X-RAY DIFFRACTION | 7 | CHAIN B AND (RESSEQ 17:43)8 | X-RAY DIFFRACTION | 8 | CHAIN B AND (RESSEQ 44:50)9 | X-RAY DIFFRACTION | 9 | CHAIN B AND (RESSEQ 51:67)10 | X-RAY DIFFRACTION | 10 | CHAIN B AND (RESSEQ 68:77)11 | X-RAY DIFFRACTION | 11 | CHAIN B AND (RESSEQ 78:96)12 | X-RAY DIFFRACTION | 12 | CHAIN B AND (RESSEQ 97:129) | | | | | | | | | | | |
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