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 | XSCALE | | データスケーリング | PDB_EXTRACT | 3.22 | データ抽出 | XDS | | データ削減 | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.3→47.978 Å / SU ML: 0.31 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.21
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2415 | 2911 | 5 % |
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Rwork | 0.2116 | - | - |
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obs | 0.2131 | 58188 | 91.99 % |
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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: 143.68 Å2 / Biso mean: 52.2446 Å2 / Biso min: 21.95 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.3→47.978 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 8045 | 0 | 72 | 81 | 8198 |
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Biso mean | - | - | 58.59 | 38.18 | - |
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残基数 | - | - | - | - | 1076 |
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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 | 8324 | X-RAY DIFFRACTION | f_angle_d0.674 | 11330 | X-RAY DIFFRACTION | f_chiral_restr0.028 | 1258 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1486 | X-RAY DIFFRACTION | f_dihedral_angle_d11.966 | 2897 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | Rms | タイプ |
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1 | 1 | A2750 | X-RAY DIFFRACTION | 5.195 | TORSIONAL1 | 2 | B2750 | X-RAY DIFFRACTION | 5.195 | TORSIONAL2 | 1 | E792 | X-RAY DIFFRACTION | 5.195 | TORSIONAL2 | 2 | F792 | X-RAY DIFFRACTION | 5.195 | TORSIONAL | | | | | | | |
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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: 21 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.2993-2.337 | 0.3944 | 122 | 0.3749 | 2304 | 2426 | 80 | 2.337-2.3773 | 0.3023 | 140 | 0.3105 | 2673 | 2813 | 95 | 2.3773-2.4205 | 0.3609 | 142 | 0.3052 | 2684 | 2826 | 94 | 2.4205-2.4671 | 0.323 | 141 | 0.2978 | 2671 | 2812 | 94 | 2.4671-2.5175 | 0.2683 | 138 | 0.2853 | 2628 | 2766 | 93 | 2.5175-2.5722 | 0.3364 | 137 | 0.2945 | 2608 | 2745 | 91 | 2.5722-2.632 | 0.3246 | 141 | 0.279 | 2680 | 2821 | 94 | 2.632-2.6978 | 0.3129 | 141 | 0.2869 | 2675 | 2816 | 95 | 2.6978-2.7708 | 0.2881 | 142 | 0.2726 | 2693 | 2835 | 94 | 2.7708-2.8523 | 0.3108 | 140 | 0.2672 | 2672 | 2812 | 94 | 2.8523-2.9443 | 0.3006 | 141 | 0.2599 | 2678 | 2819 | 94 | 2.9443-3.0496 | 0.2897 | 142 | 0.2532 | 2690 | 2832 | 94 | 3.0496-3.1716 | 0.2496 | 140 | 0.2344 | 2671 | 2811 | 93 | 3.1716-3.316 | 0.2683 | 136 | 0.2244 | 2581 | 2717 | 91 | 3.316-3.4907 | 0.2299 | 140 | 0.2114 | 2647 | 2787 | 92 | 3.4907-3.7094 | 0.2556 | 139 | 0.2011 | 2650 | 2789 | 93 | 3.7094-3.9956 | 0.2336 | 140 | 0.1854 | 2652 | 2792 | 92 | 3.9956-4.3975 | 0.1949 | 138 | 0.1574 | 2636 | 2774 | 91 | 4.3975-5.0332 | 0.152 | 135 | 0.1424 | 2556 | 2691 | 89 | 5.0332-6.339 | 0.1977 | 139 | 0.1683 | 2637 | 2776 | 91 | 6.339-47.988 | 0.1894 | 137 | 0.1682 | 2591 | 2728 | 88 |
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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 | 1.9921 | 0.6158 | -1.1619 | 1.1323 | -0.5919 | 1.5598 | -0.0521 | -0.1843 | 0.0014 | 0.0562 | 0.0441 | 0.0149 | -0.0029 | -0.006 | -0.0352 | 0.4367 | 0.0379 | -0.0194 | 0.3213 | -0.0211 | 0.2383 | -36.6067 | -32.4083 | 25.5636 | 2 | 1.5871 | 0.1943 | 0.8581 | 2.1478 | 0.58 | 1.3689 | 0.0079 | -0.3842 | -0.0373 | 0.409 | -0.0437 | 0.0627 | -0.0704 | -0.0976 | 0.0412 | 0.473 | 0.0303 | 0.0437 | 0.4383 | 0.0267 | 0.2394 | -43.7313 | -38.1424 | 34.146 | 3 | 1.721 | 0.4411 | -0.5138 | 1.1138 | -0.3221 | 0.8484 | -0.0788 | -0.0785 | 0.1455 | -0.049 | -0.0108 | -0.0936 | -0.1598 | 0.0466 | 0.0859 | 0.3667 | 0.0244 | -0.0174 | 0.2169 | 0.0031 | 0.2185 | -29.5538 | -23.1135 | 14.3051 | 4 | 3.5661 | -0.2709 | 0.9184 | 0.624 | -0.1057 | 1.0238 | -0.0499 | 0.0264 | -0.3036 | -0.0808 | 0.032 | 0.0523 | 0.0721 | 0.0188 | 0.0039 | 0.3847 | 0.0039 | 0.0179 | 0.1763 | -0.0057 | 0.2516 | -35.7763 | -51.0689 | 11.9158 | 5 | 0.7202 | -0.0947 | 0.1263 | 1.0451 | -0.1702 | 0.9588 | -0.0428 | -0.1015 | -0.2111 | 0.0922 | 0.0619 | 0.1462 | 0.0768 | -0.0142 | -0.0265 | 0.3056 | 0.0066 | 0.048 | 0.2161 | 0.0032 | 0.2546 | -42.4569 | -52.4163 | 15.0096 | 6 | 4.0843 | -1.1877 | -0.7572 | 4.0062 | 0.306 | 4.3343 | -0.0185 | -0.3511 | -0.2417 | 0.2262 | -0.0959 | -0.4162 | 0.1797 | 0.1891 | 0.1405 | 0.3015 | 0.0423 | 0.007 | 0.3187 | 0.0902 | 0.392 | -13.4338 | -56.1623 | 20.9333 | 7 | 4.1616 | 1.2419 | 3.3293 | 6.2573 | -0.378 | 3.0027 | 0.4281 | -0.0944 | -0.3276 | -0.6335 | 0.1227 | -0.0859 | 0.0218 | 0.412 | -0.3445 | 0.655 | -0.1026 | 0.1697 | 0.6482 | -0.1831 | 0.4682 | -21.3769 | -52.0784 | -8.5901 | 8 | 3.2878 | 0.2611 | 0.572 | 4.3984 | -3.8123 | 3.7362 | 0.1941 | 0.8689 | 0.4383 | -1.3976 | 0.0637 | 0.1494 | 0.0756 | 0.3095 | -0.1014 | 0.959 | -0.1071 | 0.0112 | 0.9169 | 0.0049 | 0.445 | -25.1672 | -48.1873 | -23.0521 | 9 | 3.0517 | 1.1069 | 0.3538 | 7.0755 | 2.7347 | 4.8374 | 0.1267 | 0.2444 | -0.3153 | -0.6965 | 0.0282 | -1.2557 | -0.4307 | 0.1746 | -0.1869 | 0.2708 | 0.0687 | 0.0503 | 0.3126 | 0.0029 | 0.3229 | -23.209 | -42.3816 | -0.8953 | 10 | 2.7095 | 1.6881 | 2.5937 | 4.9674 | -0.7817 | 5.8973 | 0.6882 | 0.6338 | -0.2577 | -1.1947 | -0.11 | -1.0554 | -0.3481 | 0.6044 | -0.5763 | 0.6772 | -0.0026 | 0.2325 | 0.5588 | -0.055 | 0.5041 | -11.5983 | -46.3368 | -18.265 | 11 | 2.792 | -3.5334 | -4.6982 | 4.7171 | 6.1251 | 8.0545 | 0.5402 | -0.4527 | 0.4925 | -0.7452 | 0.3153 | -0.9079 | -1.2211 | 0.2829 | -0.6028 | 0.7386 | -0.0275 | 0.0252 | 0.3641 | 0.0448 | 0.4653 | -16.8638 | -35.2242 | -12.1891 | 12 | 3.9302 | 0.0895 | -1.0558 | 0.8758 | 1.4343 | 7.8358 | 0.0558 | 1.438 | 0.4674 | -1.2905 | 0.2247 | -0.1228 | -0.5932 | -0.3585 | -0.228 | 1.208 | 0.0526 | 0.1197 | 0.7265 | 0.0897 | 0.4002 | -19.8378 | -36.1122 | -20.3863 | 13 | 3.927 | 0.9876 | -1.2877 | 3.1917 | 2.4528 | 3.0623 | 0.2689 | 0.9823 | 0.2653 | -0.8364 | -0.4048 | 0.2276 | 0.4288 | -1.0832 | 0.2262 | 0.7862 | 0.1438 | 0.0167 | 0.6835 | -0.035 | 0.3538 | -27.019 | -42.6396 | -12.9275 | 14 | 6.5732 | -1.0121 | -5.9669 | 1.1603 | 1.6789 | 6.0503 | -0.4611 | 0.2642 | 0.2866 | -1.0924 | 0.5644 | 0.0427 | -0.7299 | -0.649 | -0.1077 | 1.3359 | 0.2158 | 0.0141 | 1.444 | -0.0333 | 0.5206 | -18.8167 | -43.9197 | -30.6411 | 15 | 1.2563 | 0.1281 | 2.6461 | 3.7569 | 2.885 | 7.4963 | -0.3643 | 0.6919 | -0.5956 | -0.0856 | -0.1805 | -0.2821 | 0.3589 | 0.1205 | 0.5532 | 0.6506 | -0.0303 | 0.2427 | 0.6081 | -0.1017 | 0.3707 | -15.4095 | -45.8342 | -12.1756 | 16 | 3.8116 | 0.7282 | 2.3543 | 4.1986 | 2.4038 | 6.9732 | 0.1367 | 0.7299 | -0.9495 | -0.5435 | 0.6608 | -0.5889 | 0.1223 | 0.5464 | -0.5443 | 0.4386 | -0.0177 | 0.1951 | 0.4988 | -0.0937 | 0.5173 | -15.9788 | -49.9654 | -14.5788 | 17 | 9.7499 | -5.6168 | 3.7182 | 6.3935 | -2.5786 | 8.1744 | 0.7522 | -0.5014 | 0.4293 | -0.3492 | -0.0996 | -0.9463 | -0.3158 | 0.6207 | -0.6282 | 0.3718 | 0.0027 | 0.1797 | 0.6186 | 0.1656 | 1.0502 | 12.6313 | -65.2223 | 12.51 | 18 | 9.4071 | -1.2387 | -4.227 | 0.1654 | 0.4771 | 8.6637 | -1.378 | 0.2938 | -0.1166 | -0.0298 | 0.3096 | -0.2867 | 0.2498 | -0.2267 | 0.8685 | 0.6717 | -0.0581 | -0.0339 | 0.6046 | 0.2348 | 0.9083 | 12.0596 | -86.0584 | 20.1323 | 19 | 0.9251 | 2.7044 | -0.7535 | 8.0362 | -1.6279 | 4.8999 | -0.0029 | 0.0086 | 0.3288 | 0.2464 | -0.0605 | -0.5398 | 0.5104 | 0.4613 | 0.3135 | 0.3153 | 0.0764 | 0.1684 | 0.5001 | 0.1941 | 0.968 | 11.7075 | -69.489 | 18.8294 | 20 | 1.0635 | -0.1176 | 0.1426 | 6.5821 | 0.885 | 0.4133 | -0.0777 | 0.343 | -0.2853 | -0.7077 | 0.135 | -1.2977 | -0.0442 | 0.0131 | -0.1005 | 0.3857 | 0.065 | 0.2239 | 0.4395 | 0.1594 | 0.8395 | 3.6802 | -65.8488 | 14.8262 | 21 | 4.6805 | 1.6306 | 0.9748 | 2.0513 | -2.0439 | 4.7486 | 0.4182 | -0.0598 | 0.3764 | -0.5657 | 0.1656 | -0.0462 | -0.4748 | -0.9989 | -0.3893 | 1.0194 | -0.0554 | 0.3471 | 0.9475 | -0.3283 | 1.1244 | 0.8559 | -83.1213 | 5.0647 | 22 | 2.9806 | -1.5153 | -0.1962 | 5.5994 | 1.6026 | 5.3559 | -0.2888 | -0.2917 | -1.0501 | 0.5854 | -0.2198 | 0.919 | 0.3548 | -0.6375 | 0.4104 | 0.369 | 0.0707 | 0.1459 | 0.4531 | 0.1495 | 0.8607 | -2.7414 | -73.8276 | 20.4423 | 23 | 4.2276 | 2.124 | -0.8901 | 2.782 | -2.6243 | 3.0189 | -0.0126 | -0.7152 | -0.4215 | 1.5649 | -0.2517 | -0.586 | -0.7904 | 0.2432 | 0.2376 | 0.8403 | 0.1558 | 0.0702 | 0.595 | 0.2116 | 0.7592 | 6.5642 | -67.7508 | 24.7762 | 24 | 3.1971 | 4.5826 | -0.0906 | 9.6191 | 0.5216 | 1.1915 | -0.2127 | -0.2576 | 0.6124 | -0.2909 | -0.1601 | -0.1295 | 0.039 | 0.1764 | 0.1439 | 0.5307 | 0.0711 | -0.0115 | 0.4191 | 0.1695 | 0.774 | 8.4034 | -70.9741 | 22.3913 | 25 | 1.3382 | -1.7755 | 0.9584 | 2.7554 | -0.644 | 2.5674 | 0.139 | 0.1029 | -0.3112 | -0.7041 | -0.0368 | -0.1356 | 0.7876 | -0.1163 | -0.0603 | 0.4533 | 0.0446 | 0.197 | 0.4454 | 0.1326 | 0.853 | 4.2642 | -75.7715 | 14.6483 | 26 | 9.3499 | -4.188 | -0.8188 | 5.4015 | 0.167 | 5.2602 | -0.1542 | 0.4135 | 0.2748 | 0.5186 | 0.2914 | 0.3602 | 0.0958 | 0.1405 | -0.2164 | 0.3702 | 0.1176 | 0.149 | 0.4762 | 0.2298 | 0.6061 | -0.1463 | -55.6424 | 9.4606 | 27 | 0.8469 | -2.021 | 0.9487 | 5.4019 | -1.9916 | 1.1787 | -0.2536 | -0.1705 | -1.089 | -0.5888 | -0.0663 | 0.2273 | 0.5026 | -0.1058 | 0.2096 | 0.6937 | 0.1411 | 0.2893 | 0.4451 | 0.1264 | 1.1417 | 11.0338 | -81.4733 | 12.1248 | 28 | 6.4247 | 0.6097 | 5.0794 | 0.0759 | 0.4998 | 4.006 | -1.1188 | -1.2008 | 1.0199 | 0.3867 | -0.2242 | -0.4902 | -1.0083 | -0.4721 | 1.2085 | 0.9811 | 0.0654 | -0.14 | 1.082 | -0.0847 | 0.5558 | -8.9407 | -25.6275 | 43.8184 | 29 | 7.3801 | 2.5814 | 5.3825 | 5.1589 | 2.783 | 7.813 | -0.5598 | -0.3128 | -0.3328 | -0.2919 | 0.2676 | -0.9281 | -0.7255 | 0.5558 | 0.2913 | 0.4429 | -0.0647 | -0.0345 | 0.5491 | 0.0871 | 0.4618 | -6.4699 | -32.3058 | 34.4308 | 30 | 0.7024 | -1.4653 | -0.8451 | 3.7765 | 0.4065 | 3.7095 | 0.2124 | -1.2919 | -0.3217 | 0.4319 | -0.1752 | -1.3413 | 0.2177 | 0.7339 | -0.0083 | 0.6723 | -0.0974 | -0.3447 | 1.1012 | 0.1587 | 0.6404 | -0.5268 | -37.8204 | 40.8447 | 31 | 3.7645 | -1.5286 | 1.3037 | 1.8655 | -0.4391 | 7.5844 | -0.0364 | -1.3069 | 0.6244 | 0.8825 | -0.2176 | -1.0652 | -1.0392 | -0.1271 | 0.172 | 0.7259 | -0.1656 | -0.1912 | 0.8169 | -0.1084 | 0.7294 | -5.0319 | -28.0419 | 39.1401 | 32 | 1.8541 | -2.999 | 0.8032 | 6.9164 | -0.4955 | 2.8981 | -0.3031 | -0.1659 | 0.2403 | 0.1829 | 0.1955 | -1.0355 | -0.56 | 0.4123 | 0.0854 | 0.4002 | -0.0938 | 0.0486 | 0.3761 | 0.0784 | 0.5724 | -11.9241 | 6.5437 | 1.255 | 33 | 6.5315 | -0.7093 | -0.2162 | 7.5686 | -0.7594 | 3.2751 | -0.2945 | -0.1838 | 0.6542 | 0.729 | -0.123 | -0.264 | -0.2751 | 0.3155 | 0.3634 | 0.3225 | -0.0316 | -0.0809 | 0.2816 | 0.0809 | 0.3907 | -17.1843 | -2.5858 | 8.0843 | 34 | 7.4319 | -2.0345 | -2.0493 | 4.2399 | 0.7284 | 5.6268 | -0.2118 | 0.5369 | -0.2663 | -0.0145 | -0.0787 | -0.1839 | -0.2532 | -0.0332 | 0.3183 | 0.3492 | -0.0601 | -0.0563 | 0.3464 | 0.0103 | 0.3016 | -20.1998 | 1.7136 | 0.6185 | 35 | 2.2739 | 0.1953 | 1.7584 | 5.4245 | -3.5399 | 3.8424 | -0.3979 | -0.2363 | 0.0496 | 1.0526 | -0.0509 | -0.7209 | -0.8271 | 0.056 | 0.4475 | 0.3652 | -0.004 | -0.0522 | 0.3586 | 0.0134 | 0.396 | -16.7457 | 4.8946 | 7.9733 | 36 | 2.4108 | -1.9617 | 0.6741 | 8.1412 | -0.7814 | 1.6194 | 0.1246 | -0.0633 | 0.5202 | 0.3122 | -0.4498 | -1.1955 | -0.5888 | 0.2098 | 0.353 | 0.3713 | -0.0323 | 0.0396 | 0.3476 | 0.0523 | 0.4435 | -11.8985 | 4.2757 | 8.6531 |
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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 226 through 307 )A226 - 307 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 308 through 417 )A308 - 417 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 418 through 538 )A418 - 538 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 224 through 327 )B224 - 327 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 328 through 472 )B328 - 472 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 473 through 538 )B473 - 538 | 7 | X-RAY DIFFRACTION | 7 | chain 'E' and (resid 1 through 7 )E1 - 7 | 8 | X-RAY DIFFRACTION | 8 | chain 'E' and (resid 8 through 23 )E8 - 23 | 9 | X-RAY DIFFRACTION | 9 | chain 'E' and (resid 24 through 32 )E24 - 32 | 10 | X-RAY DIFFRACTION | 10 | chain 'E' and (resid 33 through 45 )E33 - 45 | 11 | X-RAY DIFFRACTION | 11 | chain 'E' and (resid 46 through 56 )E46 - 56 | 12 | X-RAY DIFFRACTION | 12 | chain 'E' and (resid 57 through 72 )E57 - 72 | 13 | X-RAY DIFFRACTION | 13 | chain 'E' and (resid 73 through 82 )E | | | | | | | | | | | | | | | | | | | | | | | | | |
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