ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.10.1_2155)精密化 | XDS | | データ削減 | XDS | | データスケーリング | SHARP | | 位相決定 | |
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精密化 | 構造決定の手法: 単一同系置換・異常分散 / 解像度: 2.5→49.08 Å / SU ML: 0.35 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 23.48
| Rfactor | 反射数 | %反射 |
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Rfree | 0.223 | 4029 | 4.94 % |
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Rwork | 0.1785 | - | - |
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obs | 0.1807 | 81564 | 99.78 % |
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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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精密化ステップ | サイクル: LAST / 解像度: 2.5→49.08 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 14590 | 0 | 93 | 121 | 14804 |
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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_d0.008 | 15122 | X-RAY DIFFRACTION | f_angle_d0.927 | 20541 | X-RAY DIFFRACTION | f_dihedral_angle_d10.439 | 8886 | X-RAY DIFFRACTION | f_chiral_restr0.054 | 2150 | X-RAY DIFFRACTION | f_plane_restr0.006 | 2662 | | | | | |
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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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2.4999-2.5293 | 0.4266 | 144 | 0.3726 | 2570 | X-RAY DIFFRACTION | 97 | 2.5293-2.5602 | 0.3111 | 136 | 0.2786 | 2646 | X-RAY DIFFRACTION | 100 | 2.5602-2.5926 | 0.3497 | 146 | 0.2624 | 2655 | X-RAY DIFFRACTION | 100 | 2.5926-2.6267 | 0.3086 | 136 | 0.2587 | 2625 | X-RAY DIFFRACTION | 100 | 2.6267-2.6627 | 0.3447 | 149 | 0.2919 | 2626 | X-RAY DIFFRACTION | 100 | 2.6627-2.7007 | 0.4007 | 126 | 0.333 | 2648 | X-RAY DIFFRACTION | 99 | 2.7007-2.741 | 0.3097 | 142 | 0.2664 | 2635 | X-RAY DIFFRACTION | 100 | 2.741-2.7838 | 0.3124 | 132 | 0.2537 | 2636 | X-RAY DIFFRACTION | 100 | 2.7838-2.8295 | 0.2825 | 145 | 0.2254 | 2645 | X-RAY DIFFRACTION | 100 | 2.8295-2.8782 | 0.2512 | 134 | 0.213 | 2683 | X-RAY DIFFRACTION | 100 | 2.8782-2.9306 | 0.2816 | 142 | 0.2221 | 2642 | X-RAY DIFFRACTION | 100 | 2.9306-2.9869 | 0.2948 | 156 | 0.2207 | 2627 | X-RAY DIFFRACTION | 100 | 2.9869-3.0479 | 0.2605 | 138 | 0.2064 | 2654 | X-RAY DIFFRACTION | 100 | 3.0479-3.1142 | 0.2479 | 135 | 0.2174 | 2666 | X-RAY DIFFRACTION | 100 | 3.1142-3.1866 | 0.2775 | 124 | 0.214 | 2666 | X-RAY DIFFRACTION | 100 | 3.1866-3.2663 | 0.2644 | 139 | 0.2107 | 2655 | X-RAY DIFFRACTION | 100 | 3.2663-3.3546 | 0.2648 | 136 | 0.2085 | 2683 | X-RAY DIFFRACTION | 100 | 3.3546-3.4532 | 0.2659 | 141 | 0.2281 | 2658 | X-RAY DIFFRACTION | 100 | 3.4532-3.5647 | 0.2769 | 151 | 0.1938 | 2648 | X-RAY DIFFRACTION | 100 | 3.5647-3.692 | 0.2392 | 141 | 0.1964 | 2669 | X-RAY DIFFRACTION | 100 | 3.692-3.8398 | 0.192 | 154 | 0.1686 | 2670 | X-RAY DIFFRACTION | 100 | 3.8398-4.0145 | 0.1925 | 135 | 0.1526 | 2660 | X-RAY DIFFRACTION | 99 | 4.0145-4.226 | 0.167 | 125 | 0.1356 | 2691 | X-RAY DIFFRACTION | 100 | 4.226-4.4906 | 0.1745 | 118 | 0.1299 | 2737 | X-RAY DIFFRACTION | 100 | 4.4906-4.8371 | 0.1696 | 122 | 0.1259 | 2731 | X-RAY DIFFRACTION | 100 | 4.8371-5.3233 | 0.19 | 137 | 0.1404 | 2717 | X-RAY DIFFRACTION | 100 | 5.3233-6.0924 | 0.1888 | 140 | 0.1586 | 2740 | X-RAY DIFFRACTION | 100 | 6.0924-7.671 | 0.1771 | 147 | 0.1513 | 2783 | X-RAY DIFFRACTION | 100 | 7.671-49.0897 | 0.1618 | 158 | 0.1294 | 2869 | 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 | 7.8482 | -7.1544 | -0.9545 | 8.1883 | -0.3538 | 8.627 | 0.1885 | 0.0826 | 0.6666 | 0.6129 | -0.3814 | -0.3482 | -0.798 | 0.3754 | 0.2503 | 0.6685 | -0.1244 | 0.036 | 0.3648 | -0.0505 | 0.4378 | 88.8031 | 106.3606 | 85.053 | 2 | 4.5958 | 2.2973 | -1.0824 | 6.2071 | -1.2556 | 4.3126 | 0.0589 | 0.3862 | -0.3274 | -0.4544 | -0.1996 | 0.3287 | 0.2697 | -0.2446 | 0.1503 | 0.3618 | 0.0929 | -0.0255 | 0.3741 | -0.0713 | 0.385 | 76.1276 | 90.5326 | 73.0323 | 3 | 2.1511 | -0.0187 | 0.32 | 4.6267 | -0.6761 | 3.6552 | 0.1384 | 0.1105 | -0.2041 | 0.2559 | 0.2104 | 0.8195 | 0.0096 | -0.5161 | -0.3312 | 0.3515 | 0.0512 | 0.1021 | 0.4321 | 0.0369 | 0.5861 | 65.4344 | 91.6318 | 83.4981 | 4 | 5.0451 | -0.7154 | 1.2086 | 2.7043 | -1.9725 | 5.6875 | 0.0934 | -0.3693 | -0.2397 | 0.6209 | 0.1759 | 0.8929 | -0.2742 | -0.404 | -0.2229 | 0.6282 | 0.1078 | 0.3453 | 0.4948 | 0.0215 | 0.8163 | 58.7468 | 95.728 | 96.0253 | 5 | 2.2707 | -0.7606 | 3.3979 | 9.2722 | -0.5172 | 9.8725 | 0.1706 | -1.4969 | -0.3586 | 0.9205 | -0.0752 | 1.0152 | -0.6733 | -0.6534 | 0.022 | 0.821 | -0.0003 | 0.2198 | 0.7038 | -0.0041 | 0.6147 | 70.9702 | 85.245 | 109.209 | 6 | 2.0702 | 0.8025 | 0.4141 | 2.2445 | -1.1314 | 2.2809 | 0.1763 | -0.2573 | 0.086 | 0.6601 | -0.1009 | 0.1387 | -0.3012 | -0.0085 | -0.0705 | 0.5734 | -0.0092 | 0.0325 | 0.3455 | -0.0752 | 0.3449 | 82.6442 | 95.4089 | 94.0699 | 7 | 4.0605 | 0.2775 | 0.5725 | 3.7319 | 1.2149 | 3 | 0.117 | -0.0275 | -0.0523 | 0.158 | 0.0644 | -0.2393 | -0.0798 | -0.0144 | -0.1853 | 0.4782 | 0.0206 | 0.0364 | 0.3457 | -0.0432 | 0.3524 | 71.1333 | 64.253 | 102.9492 | 8 | 5.4637 | 3.6836 | 1.1457 | 8.6335 | 0.8343 | 4.9635 | -0.0434 | 0.1298 | 0.3174 | 0.2028 | -0.0908 | 0.9175 | -0.0794 | -0.7763 | 0.1414 | 0.4809 | 0.0406 | 0.1399 | 0.4661 | -0.0759 | 0.469 | 55.2811 | 58.1441 | 106.9925 | 9 | 7.7733 | -5.227 | -4.0542 | 8.3926 | 5.2026 | 3.5821 | -0.3501 | 0.1243 | -0.8055 | 0.9669 | -0.1717 | 0.5671 | 0.5379 | -0.3721 | 0.5449 | 0.8061 | -0.0226 | 0.14 | 0.5406 | -0.0293 | 0.5256 | 62.4755 | 41.9075 | 108.3148 | 10 | 2.227 | -0.3185 | -0.1223 | 4.1882 | -0.0499 | 2.8617 | -0.0303 | -0.2093 | -0.0343 | 0.6239 | 0.1812 | -0.3951 | 0.435 | 0.4471 | -0.1355 | 0.6888 | 0.1136 | -0.1045 | 0.5694 | -0.0908 | 0.3849 | 80.3064 | 52.1466 | 109.9597 | 11 | 7.2976 | 5.2651 | 2.8856 | 6.2963 | 2.8643 | 2.3505 | -0.3619 | 0.8415 | -0.7571 | -0.8358 | 0.4741 | -0.9736 | 0.2101 | 0.6053 | -0.1538 | 0.5938 | -0.0063 | 0.092 | 0.4357 | -0.0772 | 0.5551 | 89.458 | 34.7187 | 37.7025 | 12 | 2.1267 | -0.1278 | 0.7075 | 3.9054 | -0.6782 | 1.611 | -0.0942 | -0.1602 | 0.1407 | -0.0811 | 0.135 | 0.6514 | 0.0739 | -0.3969 | -0.0335 | 0.3223 | -0.0794 | -0.0485 | 0.4887 | -0.0064 | 0.49 | 66.6042 | 46.5629 | 45.7819 | 13 | 5.6509 | 3.7337 | 0.4716 | 6.7606 | -0.1699 | 0.5612 | -0.1742 | 0.1879 | 0.4472 | -0.9635 | 0.0229 | 0.7212 | 0.1516 | -0.283 | 0.1841 | 0.5725 | -0.0314 | -0.2063 | 0.5653 | 0.0575 | 0.4951 | 68.3451 | 59.5259 | 28.5982 | 14 | 2.4884 | 0.5555 | -0.871 | 3.5536 | -0.7128 | 2.4583 | -0.01 | 0.2248 | -0.007 | -0.4987 | 0.0337 | -0.0386 | 0.1308 | 0.0886 | -0.0199 | 0.3684 | -0.0011 | -0.0033 | 0.3618 | -0.0562 | 0.3176 | 84.8246 | 49.288 | 35.7329 | 15 | 4.4023 | -3.8794 | 4.8312 | 5.9751 | -3.4941 | 5.5332 | 0.0917 | 0.7491 | 0.2452 | -0.5647 | 0.3436 | -0.1886 | -0.4197 | 0.5752 | -0.33 | 0.5062 | -0.1223 | 0.0778 | 0.6296 | -0.0088 | 0.3911 | 91.9657 | 87.8775 | 35.1953 | 16 | 0.9272 | -1.1737 | -1.8887 | 2.9024 | 1.661 | 5.656 | 0.0881 | -0.1523 | -0.2169 | 0.1548 | 0.0465 | 0.454 | 0.4728 | 0.106 | -0.1221 | 0.3342 | -0.0269 | -0.0875 | 0.4055 | 0.0239 | 0.49 | 77.2745 | 72.9617 | 46.1806 | 17 | 2.1545 | 0.0439 | -0.7059 | 2.4692 | 0.3074 | 8.0467 | -0.0894 | -0.0375 | 0.0398 | -0.0634 | -0.0138 | 0.5847 | -0.1746 | -0.6623 | 0.0706 | 0.3076 | -0.0017 | -0.1045 | 0.4823 | 0.0538 | 0.5893 | 68.2556 | 82.9627 | 48.9009 | 18 | 1.8539 | -1.519 | -2.4652 | 3.5672 | 2.0053 | 5.1919 | -0.035 | 0.183 | -0.1625 | -0.3336 | -0.2633 | 0.9642 | -0.327 | -0.9327 | 0.3334 | 0.3378 | 0.0391 | -0.176 | 0.6113 | -0.0093 | 0.7332 | 60.4882 | 89.8582 | 44.5863 | 19 | 6.8936 | 0.9573 | 5.4625 | 2.0551 | 1.7236 | 8.1133 | -0.0834 | -0.2457 | 0.4818 | -0.1987 | -0.0204 | 0.4873 | -0.5728 | -0.7 | 0.1229 | 0.4249 | 0.09 | -0.0313 | 0.3862 | 0.0021 | 0.5731 | 68.1948 | 102.855 | 53.9038 | 20 | 3.8464 | -1.0665 | -1.0481 | 4.445 | 0.4816 | 4.2005 | -0.0463 | -0.0835 | 0.2753 | -0.1226 | 0.1883 | -0.2061 | -0.326 | 0.1995 | -0.1381 | 0.3243 | -0.0752 | -0.027 | 0.2841 | -0.0092 | 0.3258 | 86.9952 | 99.0698 | 50.3853 | 21 | 3.2011 | 1.3914 | -1.1152 | 5.4488 | 5.4457 | 7.9973 | -0.1279 | -0.2923 | -0.6151 | 0.3098 | 0.4614 | -0.4613 | 0.1692 | 1.0657 | -0.3961 | 0.3186 | 0.0879 | -0.0432 | 0.4473 | 0.0473 | 0.3855 | 90.7436 | 77.8339 | 48.7206 | 22 | 4.6924 | -0.369 | -3.3121 | 6.3647 | 1.8838 | 4.9314 | 0.1779 | 0.4938 | 0.1012 | -0.7903 | 0.1833 | 0.3682 | -0.189 | -0.2563 | -0.3464 | 0.371 | -0.0656 | -0.0532 | 0.3657 | 0.0284 | 0.4014 | 77.4694 | 89.9006 | 38.9265 | 23 | 4.7881 | 4.2524 | -4.6118 | 3.8262 | -4.0583 | 4.4633 | 0.0272 | -0.2677 | -0.6118 | 0.3898 | -0.2686 | -0.133 | 0.2081 | 0.6245 | 0.2317 | 0.5537 | 0.0445 | -0.0317 | 0.4834 | 0.0099 | 0.5016 | 85.3247 | 19.7936 | 88.0972 | 24 | 2.7133 | -1.0587 | 2.2 | 0.8674 | -1.8172 | 3.891 | -0.0408 | -0.1337 | 0.2808 | 0.1787 | 0.013 | 0.1746 | -0.2509 | 0.0283 | 0.026 | 0.4673 | -0.0262 | -0.0103 | 0.4091 | -0.0956 | 0.535 | 73.1951 | 40.1764 | 87.0182 | 25 | 2.23 | -0.7269 | 1.0469 | 4.28 | -2.1163 | 5.2012 | -0.0657 | 0.0337 | 0.2941 | -0.112 | -0.0284 | 0.3328 | -0.1728 | -0.6561 | 0.1144 | 0.343 | 0.013 | 0.0117 | 0.486 | -0.0838 | 0.6144 | 64.1395 | 34.9978 | 78.0853 | 26 | 4.7166 | -1.283 | 3.4092 | 3.7939 | -2.3513 | 3.2346 | -0.1879 | -0.2557 | 0.1095 | 0.2296 | 0.2398 | 0.7889 | 0.1909 | -1.1776 | -0.0514 | 0.4092 | -0.0258 | 0.0181 | 0.6225 | -0.1273 | 0.7011 | 55.4142 | 27.8728 | 76.8526 | 27 | 6.8958 | 1.6804 | -4.5661 | 2.1265 | -0.829 | 6.4769 | -0.1477 | 0.665 | -0.0009 | -0.3699 | 0.2351 | 0.4268 | 0.3624 | -0.5291 | -0.1065 | 0.3793 | -0.0427 | -0.1125 | 0.4548 | -0.0187 | 0.4967 | 63.7101 | 22.1089 | 62.1614 | 28 | 3.4043 | 1.2061 | 0.4601 | 2.222 | -0.3773 | 3.4621 | -0.0299 | 0.1171 | -0.1804 | -0.1643 | -0.0782 | -0.1415 | 0.2676 | 0.2128 | 0.1119 | 0.461 | 0.0414 | 0.0311 | 0.3232 | -0.0105 | 0.4413 | 81.9724 | 20.716 | 68.9009 | 29 | 1.9092 | -2.4094 | 0.4367 | 3.5779 | -0.6454 | 6.5195 | -0.1671 | -0.1463 | 0.3054 | 0.0513 | 0.2426 | -0.3122 | -0.3265 | 0.6321 | -0.0305 | 0.393 | -0.0222 | -0.0463 | 0.3313 | -0.064 | 0.6156 | 86.4864 | 36.1744 | 83.3343 | 30 | 7.4531 | 0.9137 | -1.8175 | 7.3529 | -1.8277 | 2.4226 | 0.1483 | -0.9422 | -0.6631 | 0.6947 | -0.1563 | 0.5792 | 0.5837 | -0.1424 | -0.1437 | 0.4996 | -0.0431 | 0.0181 | 0.5451 | -0.0195 | 0.412 | 71.1861 | 22.2823 | 83.1148 |
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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 1 through 24 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 25 through 59 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 60 through 139 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 140 through 210 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 211 through 237 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 238 through 366 )7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 1 through 122 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 123 through 162 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 163 through 237 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 238 through 366 )11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 1 through 24 )12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 25 through 162 )13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 163 through 237 )14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resid 238 through 365 )15 | X-RAY DIFFRACTION | 15 | chain 'D' and (resid 1 through 24 )16 | X-RAY DIFFRACTION | 16 | chain 'D' | | | | | | | | | | | | | | | |
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