ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.9_1692精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | SHELX | | 位相決定 | SHARP | | 位相決定 | 直接法 | | 位相決定 | |
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精密化 | 解像度: 3.2→19.946 Å / SU ML: 0.54 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 39.96 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.308 | 973 | 4.85 % |
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Rwork | 0.2584 | - | - |
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obs | 0.2609 | 20070 | 99.46 % |
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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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精密化ステップ | サイクル: LAST / 解像度: 3.2→19.946 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4346 | 0 | 66 | 0 | 4412 |
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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_d0.003 | 4502 | X-RAY DIFFRACTION | f_angle_d0.744 | 6113 | X-RAY DIFFRACTION | f_dihedral_angle_d12.861 | 1557 | X-RAY DIFFRACTION | f_chiral_restr0.026 | 746 | X-RAY DIFFRACTION | f_plane_restr0.004 | 754 | | | | | |
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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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3.2002-3.3681 | 0.4713 | 164 | 0.3749 | 2681 | X-RAY DIFFRACTION | 99 | 3.3681-3.578 | 0.3608 | 120 | 0.3305 | 2718 | X-RAY DIFFRACTION | 99 | 3.578-3.8525 | 0.3155 | 148 | 0.304 | 2697 | X-RAY DIFFRACTION | 99 | 3.8525-4.2368 | 0.2968 | 109 | 0.2701 | 2768 | X-RAY DIFFRACTION | 100 | 4.2368-4.8422 | 0.3022 | 144 | 0.2502 | 2723 | X-RAY DIFFRACTION | 100 | 4.8422-6.072 | 0.3298 | 149 | 0.2699 | 2742 | X-RAY DIFFRACTION | 100 | 6.072-19.9461 | 0.272 | 139 | 0.2178 | 2768 | X-RAY DIFFRACTION | 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 | 0.0326 | -0.4467 | 0.0384 | 0.6677 | -0.8352 | 0.7999 | -0.0412 | -0.1826 | 0.0422 | 0.1594 | 0.1012 | -0.0797 | 0.0218 | 0.4797 | 0 | 1.0398 | -0.0331 | -0.0172 | 0.9699 | -0.0016 | 0.9964 | 61.5831 | 20.9199 | 65.5601 | 2 | -0.1985 | 0.4887 | 1.1164 | 0.9901 | -0.8647 | 0.6976 | -0.1451 | 0.4088 | -0.0839 | -0.0784 | 0.1109 | 0.0812 | -0.4861 | 0.2352 | -0 | 1.2029 | -0.2475 | 0.0956 | 0.9703 | -0.005 | 1.0996 | 55.1688 | 37.8176 | 63.9227 | 3 | 0.6046 | 0.2529 | -0.1402 | 0.5941 | 0.2744 | 3.4776 | -0.1262 | 0.3063 | -0.0807 | 0.0244 | 0.0251 | -0.0666 | -0.086 | 0.1477 | 0 | 1.0132 | -0.0465 | 0.0208 | 1.011 | 0.0312 | 1.0343 | 54.8087 | 24.447 | 62.9745 | 4 | 0.6284 | -0.0522 | 0.3579 | 0.9862 | 0.3636 | 0.0823 | -0.3326 | 0.6194 | -0.3151 | -0.1643 | 0.2337 | 0.097 | 0.2129 | 0.2922 | 0 | 1.1872 | -0.0936 | -0.0422 | 1.578 | -0.0289 | 1.2573 | 11.3875 | 18.0669 | 43.6704 | 5 | 0.1548 | -0.1296 | -0.1766 | 0.0732 | -0.2098 | -0.3574 | -0.088 | -0.6374 | 0.1162 | 0.6134 | 0.6873 | -0.6881 | -0.7305 | -1.1012 | 0 | 1.6777 | 0.1669 | 0.0598 | 1.8434 | -0.2265 | 2.0201 | -10.8884 | 28.476 | 61.5456 | 6 | 0.147 | -0.0782 | 0.1215 | 0.1523 | 0.3404 | -0.0255 | 0.1285 | -1.7622 | 0.9169 | 0.7473 | 0.9533 | 0.6081 | -0.4728 | -0.4612 | 0 | 1.3492 | 0.2287 | -0.0894 | 1.7192 | -0.2371 | 1.6303 | 2.6123 | 28.5349 | 56.5889 | 7 | 0.1195 | 0.0138 | -0.0511 | 0.0416 | -0.0662 | -0.1276 | -0.7786 | -0.978 | -0.323 | 0.2117 | -0.1496 | -0.4216 | -0.5254 | -0.5689 | -0 | 1.6354 | 0.0011 | 0.2333 | 2.0615 | 0.1405 | 1.8061 | -2.3522 | 22.1376 | 49.7368 | 8 | -0.0406 | 0.0034 | -0.0363 | -0.0029 | 0.0458 | 0.0191 | -0.2337 | 0.1303 | 0.3082 | -0.197 | 0.0599 | 0.4435 | 0.1419 | -0.1268 | 0 | 2.0041 | 0.4665 | -0.0902 | 2.4694 | -0.3483 | 1.8382 | -6.9484 | 36.2494 | 48.4585 | 9 | 0.1643 | -0.0745 | -0.0301 | 0.1603 | 0.0688 | -0.019 | 0.1887 | -0.7748 | 0.7812 | -0.0534 | -0.4165 | -0.0094 | 0.9693 | 0.3476 | -0 | 1.5728 | 0.0252 | -0.0555 | 1.821 | -0.1493 | 1.6461 | -5.5257 | 24.708 | 59.6944 | 10 | -0.016 | 0.2922 | 0.0916 | -0.0205 | -0.0223 | -0.1148 | -0.7294 | -0.8133 | 0.6628 | -0.0405 | 0.5448 | -0.4185 | 0.1159 | 0.2241 | 0 | 1.9477 | -0.0157 | -0.0783 | 2.767 | -0.2764 | 2.2111 | 4.3738 | 31.7071 | 57.3173 |
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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 (resid 14 through 113 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 114 through 191 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 192 through 391 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 392 through 484 )5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 9 through 26 )6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 27 through 55 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 56 through 71 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 72 through 80 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 81 through 100 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 101 through 124 ) | | | | | | | | | |
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