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 | PHASER | 2.5.7位相決定 | PDB_EXTRACT | 3.15 | データ抽出 | XDS | | データ削減 | XSCALE | | 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: 4ZEM and 4ZEO 解像度: 3→48.948 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 26.61 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2546 | 1554 | 5 % |
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Rwork | 0.2082 | - | - |
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obs | 0.2105 | 31060 | 99.66 % |
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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→48.948 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 9377 | 0 | 0 | 0 | 9377 |
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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_d0.007 | 9564 | X-RAY DIFFRACTION | f_angle_d1.316 | 12970 | X-RAY DIFFRACTION | f_dihedral_angle_d14.257 | 3538 | X-RAY DIFFRACTION | f_chiral_restr0.053 | 1506 | X-RAY DIFFRACTION | f_plane_restr0.007 | 1688 | | | | | |
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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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3.0002-3.097 | 0.3521 | 136 | 0.3134 | 2579 | X-RAY DIFFRACTION | 97 | 3.097-3.2077 | 0.3263 | 139 | 0.2924 | 2644 | X-RAY DIFFRACTION | 100 | 3.2077-3.3361 | 0.2842 | 139 | 0.2595 | 2627 | X-RAY DIFFRACTION | 100 | 3.3361-3.4879 | 0.2764 | 140 | 0.2491 | 2668 | X-RAY DIFFRACTION | 100 | 3.4879-3.6717 | 0.2845 | 140 | 0.2313 | 2657 | X-RAY DIFFRACTION | 100 | 3.6717-3.9016 | 0.279 | 140 | 0.2209 | 2659 | X-RAY DIFFRACTION | 100 | 3.9016-4.2027 | 0.2597 | 141 | 0.2028 | 2672 | X-RAY DIFFRACTION | 100 | 4.2027-4.6254 | 0.2224 | 141 | 0.1753 | 2682 | X-RAY DIFFRACTION | 100 | 4.6254-5.294 | 0.1995 | 142 | 0.1762 | 2702 | X-RAY DIFFRACTION | 100 | 5.294-6.6672 | 0.2783 | 144 | 0.2108 | 2736 | X-RAY DIFFRACTION | 100 | 6.6672-48.954 | 0.2381 | 152 | 0.1836 | 2880 | 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 | 2.3762 | 2.3059 | 0.6207 | 5.0495 | 2.2413 | 0.9058 | -0.1371 | -0.1389 | -0.6759 | 0.7903 | 0.2249 | -0.7782 | 0.2733 | 0.6638 | -0.0814 | 0.6188 | -0.0607 | -0.1188 | 0.6167 | 0.0234 | 1.3198 | 42.2395 | -22.9009 | -14.5994 | 2 | 4.9852 | 0.1616 | -0.0775 | 3.7003 | -0.9301 | 3.8513 | -0.4148 | 0.6413 | -0.4896 | -0.9613 | 0.4292 | -0.6834 | -0.1944 | 0.1602 | -0.0616 | 0.6593 | -0.2517 | 0.1561 | 0.5338 | -0.1081 | 0.7147 | 30.273 | -27.3796 | -28.7194 | 3 | 4.5242 | 1.0851 | 0.1163 | 6.3136 | -1.3373 | 4.616 | 0.1993 | -0.4179 | -0.7391 | -0.0841 | -0.0197 | -0.1085 | 0.4691 | -0.0607 | -0.2077 | 0.5807 | -0.1627 | -0.0885 | 0.428 | -0.0026 | 0.6792 | 21.7839 | -36.6115 | -22.1169 | 4 | 1.8852 | 2.4183 | -0.5185 | 4.0463 | 0.3095 | 1.9016 | 0.0666 | -0.0402 | 0.0046 | -0.368 | 0.0177 | 0.684 | -0.001 | 0.0121 | -0.044 | 0.4737 | -0.1369 | -0.0459 | 0.5227 | 0.0189 | 0.5142 | 17.3518 | -6.501 | -33.9093 | 5 | 2.9591 | 0.1198 | 0.2513 | 3.5522 | 0.6073 | 2.1674 | -0.151 | 0.5044 | -0.2877 | -0.6437 | 0.2568 | -0.3454 | -0.1755 | 0.3036 | -0.1583 | 0.5226 | -0.2488 | 0.0376 | 0.7099 | -0.0132 | 0.4945 | 28.0505 | 1.7435 | -33.1546 | 6 | 2.5775 | 0.683 | 1.1069 | 1.7774 | -0.2632 | 1.7376 | 0.1104 | 0.0744 | -0.3914 | 0.2281 | -0.1141 | -0.1838 | 0.1187 | -0.0514 | -0.0298 | 0.4851 | -0.0952 | -0.0253 | 0.4543 | -0.0196 | 0.3958 | 24.849 | -8.4738 | -17.5472 | 7 | 4.4643 | 0.0793 | 2.1278 | 2.9596 | 0.936 | 4.6419 | -0.2607 | 1.2844 | -0.0579 | -0.662 | 0.4026 | -0.6446 | 0.347 | 0.4867 | -0.1859 | 0.7557 | -0.2198 | 0.0927 | 0.9957 | 0.0334 | 0.7521 | 56.1602 | 32.2566 | -26.4899 | 8 | 2.0772 | 2.2009 | -1.3019 | 4.9063 | -3.6065 | 2.4373 | 0.302 | 0.2876 | 0.483 | 0.9028 | 0.1756 | -0.0712 | -0.485 | -0.1748 | -0.1432 | 0.7148 | -0.1767 | 0.0711 | 0.6576 | -0.0628 | 1.1042 | 52.1638 | 33.7991 | -12.9229 | 9 | 3.3178 | -0.0704 | 0.9057 | 4.3817 | -0.7102 | 2.2941 | 0.0576 | 0.2072 | -0.0595 | -0.0916 | -0.1063 | -0.105 | -0.1041 | 0.1743 | 0.0848 | 0.4825 | -0.2195 | -0.0214 | 0.6081 | -0.0237 | 0.4674 | 41.818 | 9.7799 | -12.0953 | 10 | 8.1897 | 3.7356 | 1.629 | 5.5069 | 1.301 | 2.8534 | 1.3316 | -0.265 | 3.2769 | 1.6755 | -0.8542 | 0.7172 | -1.4932 | -0.3595 | -0.3132 | 0.9935 | -0.009 | 0.3435 | 0.7332 | -0.0151 | 0.9551 | 38.432 | 25.9436 | -5.9999 | 11 | 0.3736 | -0.9839 | -0.4013 | 2.9848 | 0.8216 | 0.0497 | 0.1811 | -0.4802 | 0.016 | 0.6358 | -0.2672 | -0.1274 | 0.0464 | 0.3134 | 0.1593 | 0.9588 | -0.3632 | -0.214 | 0.8074 | 0.0578 | 0.7019 | 42.2864 | 19.54 | 25.8275 | 12 | 5.1901 | 5.6362 | 2.4432 | 7.9774 | 3.0832 | 1.7242 | 0.9321 | -0.4768 | -0.0598 | 0.6845 | -0.5518 | -0.6971 | 0.555 | 0.0624 | -0.2924 | 0.9542 | -0.3782 | -0.1385 | 0.7475 | 0.0233 | 1.1914 | 51.79 | 31.2101 | 24.23 | 13 | 5.1682 | 1.9095 | 0.4487 | 1.498 | -0.5761 | 0.9281 | 0.2223 | -0.011 | 1.1285 | 0.1756 | -0.1176 | 0.2062 | -0.4131 | 0.1501 | -0.0987 | 1.0481 | -0.2845 | 0.0055 | 0.6056 | -0.0631 | 0.6178 | 37.072 | 38.2578 | 19.259 | 14 | 3.1639 | -0.6962 | -1.0095 | 2.52 | 1.2604 | 1.965 | 0.0352 | -0.051 | 0.046 | 0.2187 | 0.1165 | -0.1393 | -0.2076 | 0.1239 | -0.1857 | 0.718 | -0.1389 | -0.0651 | 0.4031 | 0.0141 | 0.3535 | 21.3895 | 16.8908 | 15.9664 | 15 | 0.4702 | 0.2805 | 0.2967 | 0.1566 | 0.1889 | 0.2821 | 0.0077 | -0.6749 | -0.6437 | 0.6359 | 2.1051 | -0.918 | -0.2117 | -0.6988 | 0.2068 | 1.8244 | -0.1494 | 0.5018 | 1.4152 | 0.1072 | 1.5433 | 10.3512 | -31.5283 | 29.2436 | 16 | 1.0125 | 1.0155 | 1.2904 | 3.5583 | 1.6959 | 1.7456 | -0.5866 | -1.3028 | -0.9947 | 0.5398 | -0.288 | -0.2762 | -0.0792 | -0.7321 | 0.4893 | 2.1208 | -0.6814 | 1.4501 | 1.1628 | -0.0515 | 0.741 | 6.0294 | -21.1754 | 27.4379 | 17 | 2.1785 | -2.2559 | -0.3637 | 8.5977 | 0.8431 | 8.2044 | -0.3201 | -0.177 | -0.9671 | 1.2349 | 0.3997 | 1.6628 | 0.1424 | -0.2677 | 0.0875 | 1.1045 | -0.3374 | 0.162 | 0.7925 | 0.0163 | 1.0618 | -1.4529 | -28.635 | 18.9489 | 18 | 3.8965 | 3.8743 | 3.702 | 4.8569 | 5.0584 | 5.6114 | 0.1902 | 1.2356 | 0.0755 | 0.8375 | 0.1786 | 1.4129 | -0.2358 | -0.569 | 0.368 | 1.5131 | -0.3339 | 0.2778 | 0.6552 | 0.0061 | 1.7232 | -0.129 | -26.5247 | 9.9665 | 19 | 1.9996 | 0.488 | -1.5662 | 3.3662 | -0.3236 | 2.2518 | -0.2197 | -0.0063 | -0.5592 | 0.3195 | 0.0929 | 0.0379 | 0.4175 | -0.0024 | 0.003 | 0.6535 | -0.1147 | -0.0658 | 0.4295 | 0.0696 | 0.541 | 23.3378 | -13.9664 | 10.2697 | 20 | 2.5519 | 0.4374 | -0.6036 | 3.3569 | -0.3203 | 4.797 | 0.3285 | -0.5522 | -0.6309 | 0.3553 | -0.8489 | 1.9555 | -0.1295 | -0.7848 | 0.1451 | 0.694 | -0.1997 | 0.2427 | 0.651 | -0.0802 | 1.1469 | 10.8893 | -7.5021 | 7.8257 | 21 | 3.0992 | -1.4353 | -0.689 | 1.1816 | -0.2129 | 6.2123 | -0.7109 | 0.6077 | -0.3369 | -2.3799 | 1.1729 | 3.643 | 0.5808 | -0.8492 | -0.4595 | 0.903 | -0.2408 | -0.2442 | 0.7796 | 0.0784 | 1.3284 | 12.5338 | -14.4197 | -0.9227 |
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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 127 through 156 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 157 through 190 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 191 through 264 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 265 through 304 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 305 through 353 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 354 through 443 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 10 through 82 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 83 through 214 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 215 through 382 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 383 through 406 )11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 127 through 191 )12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 192 through 223 )13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 224 through 279 )14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 280 through 441 )15 | X-RAY DIFFRACTION | 15 | chain 'D' and (resid 10 through 23 )16 | X-RAY DIFFRACTION | 16 | chain 'D' | | | | | | | | | | | | | | | |
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