ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALEPACK | | データスケーリング | | PHENIX | 1.7.1_743精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.5→49.16 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.69 / σ(F): 1.33 / 位相誤差: 22.56 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.21 | 3462 | 5.06 % |
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Rwork | 0.167 | - | - |
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obs | 0.169 | 68418 | 99.2 % |
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溶媒の処理 | 減衰半径: 0.72 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 38.66 Å2 / ksol: 0.34 e/Å3 |
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原子変位パラメータ | Biso mean: 53.66 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.0943 Å2 | -0 Å2 | 1.1955 Å2 |
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2- | - | -1.5118 Å2 | -0 Å2 |
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3- | - | - | 1.4175 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.5→49.16 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 9699 | 0 | 60 | 214 | 9973 |
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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 | 9928 | X-RAY DIFFRACTION | f_angle_d1.106 | 13438 | X-RAY DIFFRACTION | f_dihedral_angle_d14.267 | 3723 | X-RAY DIFFRACTION | f_chiral_restr0.072 | 1536 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1736 | | | | | |
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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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2.5016-2.5359 | 0.3028 | 128 | 0.2321 | 2366 | X-RAY DIFFRACTION | 91 | 2.5359-2.5721 | 0.3432 | 129 | 0.2352 | 2574 | X-RAY DIFFRACTION | 99 | 2.5721-2.6105 | 0.2999 | 143 | 0.2169 | 2629 | X-RAY DIFFRACTION | 99 | 2.6105-2.6513 | 0.2611 | 121 | 0.2065 | 2592 | X-RAY DIFFRACTION | 99 | 2.6513-2.6948 | 0.2599 | 115 | 0.2046 | 2579 | X-RAY DIFFRACTION | 99 | 2.6948-2.7412 | 0.2741 | 124 | 0.2084 | 2645 | X-RAY DIFFRACTION | 99 | 2.7412-2.7911 | 0.2529 | 127 | 0.2198 | 2569 | X-RAY DIFFRACTION | 99 | 2.7911-2.8448 | 0.3178 | 145 | 0.2152 | 2617 | X-RAY DIFFRACTION | 100 | 2.8448-2.9028 | 0.2682 | 122 | 0.206 | 2589 | X-RAY DIFFRACTION | 99 | 2.9028-2.9659 | 0.2648 | 135 | 0.2 | 2616 | X-RAY DIFFRACTION | 100 | 2.9659-3.0349 | 0.2751 | 134 | 0.1899 | 2604 | X-RAY DIFFRACTION | 100 | 3.0349-3.1108 | 0.2407 | 143 | 0.1792 | 2595 | X-RAY DIFFRACTION | 100 | 3.1108-3.1949 | 0.2172 | 148 | 0.1809 | 2612 | X-RAY DIFFRACTION | 100 | 3.1949-3.2889 | 0.2332 | 147 | 0.1828 | 2608 | X-RAY DIFFRACTION | 100 | 3.2889-3.395 | 0.2275 | 131 | 0.1745 | 2637 | X-RAY DIFFRACTION | 100 | 3.395-3.5163 | 0.2485 | 149 | 0.1752 | 2601 | X-RAY DIFFRACTION | 100 | 3.5163-3.6571 | 0.2212 | 131 | 0.1634 | 2621 | X-RAY DIFFRACTION | 100 | 3.6571-3.8234 | 0.1756 | 156 | 0.1522 | 2601 | X-RAY DIFFRACTION | 100 | 3.8234-4.0249 | 0.1624 | 148 | 0.1388 | 2608 | X-RAY DIFFRACTION | 100 | 4.0249-4.277 | 0.1871 | 138 | 0.1347 | 2624 | X-RAY DIFFRACTION | 100 | 4.277-4.607 | 0.1524 | 148 | 0.1204 | 2610 | X-RAY DIFFRACTION | 100 | 4.607-5.0702 | 0.1745 | 155 | 0.1275 | 2626 | X-RAY DIFFRACTION | 100 | 5.0702-5.8028 | 0.1891 | 138 | 0.1711 | 2634 | X-RAY DIFFRACTION | 100 | 5.8028-7.3071 | 0.1904 | 152 | 0.1663 | 2620 | X-RAY DIFFRACTION | 100 | 7.3071-49.1649 | 0.1979 | 155 | 0.1677 | 2579 | X-RAY DIFFRACTION | 97 |
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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 | 0.0444 | -0.0337 | -0.1619 | 0.1024 | 0.1887 | 0.9463 | 0.2023 | -0.051 | -0.0646 | -0.0022 | -0.2459 | -0.2964 | -0.2557 | 0.4002 | -0.0208 | 0.2161 | -0.0068 | -0.0234 | 0.414 | 0.0295 | 0.3894 | -19.7179 | 5.9318 | 12.1959 | 2 | 0.3495 | 0.2324 | -0.2132 | 0.1969 | -0.2182 | 0.2849 | 0.0374 | -0.0939 | -0.1 | -0.0922 | 0.041 | 0.0112 | -0.0119 | 0.0919 | -0 | 0.287 | -0.0326 | -0.0139 | 0.3011 | 0.0029 | 0.2888 | -34.7774 | 8.3076 | -0.532 | 3 | 0.1133 | 0.0988 | -0.0386 | 0.0736 | -0.0057 | 0.0605 | 0.0935 | -0.0566 | -0.298 | 0.2392 | -0.0696 | 0.0994 | 0.0693 | -0.1176 | -0.0005 | 0.3701 | -0.1069 | -0.0209 | 0.3014 | 0.0398 | 0.3071 | -46.4561 | 1.2922 | 2.0278 | 4 | 0.0247 | -0.0066 | 0.0366 | 0.0802 | 0.0289 | 0.0638 | -0.3234 | 0.1288 | -0.0663 | -0.6049 | 0.1936 | 0.0846 | 0.0156 | 0.0418 | -0.0013 | 0.4658 | -0.155 | -0.0084 | 0.3882 | 0.0134 | 0.3235 | -46.5998 | 0.9007 | -13.903 | 5 | 0.0488 | -0.0714 | -0.0282 | 0.2202 | 0.0117 | 0.044 | -0.049 | 0.2821 | 0.1328 | -0.3171 | 0.0273 | -0.0854 | -0.2161 | 0.263 | 0.0001 | 0.2945 | -0.0819 | 0.0852 | 0.3532 | -0.0507 | 0.3369 | -26.0823 | 9.2073 | -5.4324 | 6 | 0.1648 | -0.2389 | 0.0785 | 0.3954 | -0.2924 | 0.4449 | 0.0615 | 0.0114 | -0.1879 | 0.0134 | -0.0537 | -0.0111 | 0.3488 | 0.1242 | 0.0001 | 0.3452 | -0.0419 | 0.0641 | 0.4794 | -0.0563 | 0.4806 | -19.0531 | -4.609 | -4.6772 | 7 | 0.2633 | 0.1809 | 0.0571 | 0.2894 | 0.1551 | 0.0762 | 0.0177 | 0.232 | -0.2965 | -0.1133 | 0.0796 | -0.0513 | 0.1674 | 0.3523 | 0.0004 | 0.3603 | 0.0182 | 0.0256 | 0.4505 | -0.0811 | 0.4811 | -22.1145 | -9.8712 | -0.8459 | 8 | 0.2825 | 0.0746 | -0.0271 | 0.0793 | 0.0112 | 0.2808 | -0.1101 | 0.1606 | -0.1444 | 0.0468 | -0.1637 | -0.2991 | 0.1892 | 0.1531 | -0.2197 | 0.1981 | 0.081 | -0.0135 | 0.4514 | -0.0175 | 0.3906 | -15.0451 | -9.3428 | 5.2194 | 9 | 0.041 | 0.0572 | -0.0294 | 0.0286 | -0.0274 | 0.0341 | 0.0092 | 0.0818 | -0.0168 | 0.0059 | -0.1589 | 0.0206 | 0.2492 | -0.1891 | -0.0003 | 0.4783 | -0.1829 | 0.017 | 0.4474 | -0.0837 | 0.4456 | -36.1583 | -12.9526 | 13.9267 | 10 | 0.1186 | 0.0828 | -0.0945 | 0.1016 | 0.0495 | 0.2039 | -0.2224 | 0.0658 | 0.0427 | 0.175 | 0.2308 | 0.0054 | -0.2732 | 0.1637 | -0 | 0.3506 | 0.0033 | 0.0067 | 0.3942 | -0.026 | 0.2693 | -26.7149 | 13.2222 | 17.524 | 11 | 0.3621 | 0.1205 | -0.2582 | 0.3669 | 0.2392 | 0.4432 | -0.1794 | -0.183 | 0.0021 | 0.1425 | 0.3322 | -0.3216 | 0.0851 | -0.088 | 0.0061 | 0.3665 | 0.0323 | -0.0569 | 0.2781 | 0.0045 | 0.2712 | -27.4963 | -2.72 | 29.2147 | 12 | 0.0506 | 0.0605 | 0.0464 | 0.0714 | 0.0468 | 0.0403 | -0.0202 | -0.0988 | 0.1935 | 0.033 | 0.1573 | 0.1949 | 0.1599 | -0.1407 | 0.0006 | 0.6299 | -0.0779 | 0.0106 | 0.4337 | 0.0938 | 0.3449 | -37.9631 | -12.6669 | 26.7039 | 13 | 0.8689 | -0.8656 | -0.0769 | 1.2223 | -0.1124 | 0.1016 | -0.0468 | -0.4112 | 0.0333 | 0.3744 | 0.1215 | -0.3497 | 0.4394 | -0.0264 | 0.051 | 0.8624 | -0.0752 | 0.0157 | 0.5476 | 0.1132 | 0.2427 | -32.5916 | -10.3408 | 40.9476 | 14 | 0.0973 | 0.019 | 0.1947 | 0.1891 | 0.2316 | 0.6092 | -0 | -0.0734 | 0.1172 | 0.1327 | 0.1443 | 0.023 | 0.0345 | -0.1028 | 0 | 0.299 | 0.0108 | 0.0052 | 0.3013 | -0.0415 | 0.2755 | -30.1956 | 16.9561 | 32.3259 | 15 | 0.0139 | 0.0186 | -0.0119 | 0.0166 | -0.0117 | 0.0068 | -0.1779 | 0.2396 | 0.2806 | 0.2263 | 0.1155 | -0.0113 | 0.1323 | -0.3906 | -0.0003 | 0.6208 | -0.2531 | 0.066 | 0.8504 | 0.0055 | 0.6112 | -47.5965 | 6.4497 | 35.1369 | 16 | 0.1222 | -0.1509 | -0.1155 | 0.2919 | 0.2226 | 0.1555 | -0.0027 | -0.1195 | 0.0189 | 0.146 | 0.0178 | 0.2149 | 0.0194 | -0.0722 | -0 | 0.2376 | -0.0354 | 0.0446 | 0.3643 | -0.0052 | 0.2822 | -42.9943 | 13.1547 | 29.2096 | 17 | 0.1349 | 0.0274 | 0.0034 | 0.078 | -0.1617 | 0.3619 | 0.0231 | -0.0724 | 0.0204 | -0.1346 | -0.0973 | -0.1743 | 0.0213 | -0.3573 | 0.0008 | 0.332 | 0.0097 | 0.0221 | 0.3155 | -0.0194 | 0.2308 | -40.5127 | 15.4505 | 22.2597 | 18 | 0.0786 | 0.0004 | -0.0214 | -0.0022 | -0.0018 | 0.0096 | 0.0541 | 0.0993 | 0.3781 | 0.0739 | -0.0816 | 0.4056 | 0.2072 | -0.3667 | -0.0006 | 0.385 | -0.191 | 0.0607 | 0.5225 | 0.0297 | 0.4808 | -53.0899 | -0.5764 | 6.0645 | 19 | 0.057 | -0.0295 | 0.1087 | 0.074 | -0.2319 | 0.386 | 0.0201 | -0.1615 | -0.1061 | -0.0792 | -0.0404 | -0.2081 | 0.181 | 0.0394 | -0.0732 | 0.1807 | 0.001 | 0.0463 | 0.3665 | -0.0464 | 0.3742 | -29.7699 | 41.6392 | 66.227 | 20 | 0.4489 | -0.3438 | -0.3001 | 0.9009 | 0.4878 | 1.4925 | 0.2186 | 0.2203 | 0.0785 | -0.2438 | 0.1188 | -0.2798 | -0.2783 | 0.0183 | 0.4619 | 0.2791 | -0.0255 | 0.1462 | 0.227 | 0.0086 | 0.2661 | -34.9762 | 50.0719 | 45.618 | 21 | 0.1076 | -0.0147 | -0.0226 | 0.4156 | -0.1716 | 0.3589 | 0.0443 | 0.1085 | 0.041 | -0.1251 | 0.0289 | -0.0303 | -0.1091 | -0.3009 | 0.0027 | 0.2588 | 0.0346 | -0.0386 | 0.3266 | 0.0153 | 0.2414 | -52.8075 | 42.2716 | 54.8211 | 22 | 0.137 | 0.0986 | -0.2575 | 0.0674 | -0.1822 | 0.7776 | 0.015 | -0.1009 | -0.0042 | -0.1065 | -0.28 | -0.4745 | 0.2512 | 0.2357 | -0.1106 | 0.2656 | -0.0377 | -0.0024 | 0.3062 | -0.0314 | 0.484 | -31.5705 | 46.8879 | 69.5599 | 23 | 0.2085 | -0.2513 | -0.1068 | 0.273 | 0.0863 | 0.1323 | 0.0235 | -0.005 | 0.1267 | 0.1478 | 0.0665 | -0.0404 | 0.0466 | 0.0699 | 0 | 0.3205 | 0.0377 | -0.0184 | 0.277 | 0.0107 | 0.3008 | -50.3616 | 44.76 | 75.0839 | 24 | 0.0901 | -0.0796 | 0.0345 | 0.0641 | -0.0461 | 0.0522 | -0.0105 | 0.2489 | 0.3149 | -0.2438 | 0.0078 | 0.1964 | 0.0999 | -0.2821 | -0.0011 | 0.3412 | 0.0774 | 0.01 | 0.3936 | 0.0659 | 0.3868 | -59.9872 | 51.851 | 68.0341 | 25 | 0.0451 | -0.0341 | 0.005 | 0.0276 | -0.0004 | 0.0067 | -0.208 | -0.3548 | 0.0214 | 0.3751 | 0.2117 | 0.1228 | -0.1362 | -0.0454 | -0 | 0.4734 | 0.1036 | 0.1396 | 0.4437 | 0.0816 | 0.4242 | -66.5375 | 52.3034 | 82.4857 | 26 | 0.0548 | 0.0656 | 0.0609 | 0.6952 | 0.3206 | 0.1647 | -0.1345 | -0.3645 | -0.241 | 0.6201 | 0.0424 | -0.1802 | 0.2512 | 0.0871 | 0.0678 | 0.4065 | 0.1024 | -0.1439 | 0.3141 | -0.0137 | 0.305 | -44.4652 | 43.8095 | 83.1011 | 27 | 0.6064 | 0.528 | -0.6399 | 0.6088 | -0.4046 | 1.5638 | 0.1203 | -0.2204 | 0.1975 | 0.4652 | 0.0111 | -0.1886 | -0.468 | -0.1052 | 0.2841 | 0.4458 | 0.039 | -0.1962 | 0.4138 | -0.0793 | 0.4314 | -38.5915 | 57.9744 | 86.4923 | 28 | 0.1638 | 0.099 | -0.1862 | 0.5154 | 0.7064 | 1.7176 | 0.1111 | -0.0004 | 0.2761 | -0.2158 | 0.1266 | -0.6919 | -0.6967 | -0.0642 | 0.3797 | 0.1715 | -0.0844 | -0.0716 | 0.2642 | -0.1337 | 0.5667 | -31.7873 | 64.0984 | 74.8473 | 29 | 0.0093 | -0.008 | 0.0122 | -0.0071 | -0.0144 | 0.0121 | 0.1595 | -0.2181 | -0.1131 | -0.1457 | -0.0469 | -0.1448 | -0.157 | -0.3628 | 0.0005 | 0.4932 | 0.1366 | 0.0236 | 0.4106 | -0.0211 | 0.4713 | -45.5374 | 65.9287 | 61.2376 |
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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 51:79 )2 | X-RAY DIFFRACTION | 2 | (CHAIN A AND RESID 80:151 )3 | X-RAY DIFFRACTION | 3 | (CHAIN A AND RESID 152:169 )4 | X-RAY DIFFRACTION | 4 | (CHAIN A AND RESID 170:187 )5 | X-RAY DIFFRACTION | 5 | (CHAIN A AND RESID 188:217 )6 | X-RAY DIFFRACTION | 6 | (CHAIN A AND RESID 218:278 )7 | X-RAY DIFFRACTION | 7 | (CHAIN A AND RESID 279:311 )8 | X-RAY DIFFRACTION | 8 | (CHAIN A AND RESID 312:344 )9 | X-RAY DIFFRACTION | 9 | (CHAIN A AND RESID 345:367 )10 | X-RAY DIFFRACTION | 10 | (CHAIN B AND RESID 52:79 )11 | X-RAY DIFFRACTION | 11 | (CHAIN B AND RESID 80:151 )12 | X-RAY DIFFRACTION | 12 | (CHAIN B AND RESID 152:172 )13 | X-RAY DIFFRACTION | 13 | (CHAIN B AND RESID 173:199 )14 | X-RAY DIFFRACTION | 14 | (CHAIN B AND RESID 200:259 )15 | X-RAY DIFFRACTION | 15 | (CHAIN B AND RESID 260:278 )16 | X-RAY DIFFRACTION | 16 | (CHAIN B AND RESID 279:311 )17 | X-RAY DIFFRACTION | 17 | (CHAIN B AND RESID 312:354 )18 | X-RAY DIFFRACTION | 18 | (CHAIN B AND | | | | | | | | | | | | | | | | | |
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