ソフトウェア | 名称 | バージョン | 分類 |
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Aimless | 0.5.27データスケーリング | PHASER | | 位相決定 | PHENIX | | 精密化 | PDB_EXTRACT | 3.24 | データ抽出 | XDS | | データ削減 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 2VQR,2W8S,3ED4, 3B5Q 解像度: 1.98→19.976 Å / SU ML: 0.2 / 交差検証法: THROUGHOUT / σ(F): 0.01 / 位相誤差: 22.3
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2 | 9987 | 5.07 % |
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Rwork | 0.1706 | - | - |
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obs | 0.1721 | 196983 | 99.64 % |
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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: 216.73 Å2 / Biso mean: 45.6141 Å2 / Biso min: 14.21 Å2 |
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精密化ステップ | サイクル: final / 解像度: 1.98→19.976 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 16015 | 0 | 74 | 861 | 16950 |
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Biso mean | - | - | 59.34 | 39.93 | - |
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残基数 | - | - | - | - | 2022 |
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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_d0.005 | 16557 | X-RAY DIFFRACTION | f_angle_d0.809 | 22596 | X-RAY DIFFRACTION | f_chiral_restr0.045 | 2382 | X-RAY DIFFRACTION | f_plane_restr0.005 | 2980 | X-RAY DIFFRACTION | f_dihedral_angle_d11.511 | 9814 | | | | | |
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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: 30 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.9784-2.0009 | 0.3259 | 680 | 0.272 | 12314 | 12994 | 100 | 2.0009-2.0244 | 0.2858 | 694 | 0.2553 | 12245 | 12939 | 99 | 2.0244-2.049 | 0.2741 | 593 | 0.2428 | 12392 | 12985 | 100 | 2.049-2.0749 | 0.268 | 664 | 0.2331 | 12378 | 13042 | 100 | 2.0749-2.1022 | 0.2766 | 667 | 0.2297 | 12330 | 12997 | 100 | 2.1022-2.131 | 0.2737 | 573 | 0.2262 | 12480 | 13053 | 100 | 2.131-2.1614 | 0.2563 | 671 | 0.2238 | 12293 | 12964 | 100 | 2.1614-2.1936 | 0.2412 | 602 | 0.2059 | 12337 | 12939 | 100 | 2.1936-2.2279 | 0.2482 | 682 | 0.2001 | 12308 | 12990 | 100 | 2.2279-2.2643 | 0.2215 | 628 | 0.189 | 12314 | 12942 | 100 | 2.2643-2.3033 | 0.2171 | 713 | 0.1789 | 12356 | 13069 | 100 | 2.3033-2.3451 | 0.2196 | 666 | 0.1784 | 12365 | 13031 | 100 | 2.3451-2.3902 | 0.2209 | 659 | 0.1793 | 12294 | 12953 | 100 | 2.3902-2.4389 | 0.2276 | 716 | 0.173 | 12256 | 12972 | 100 | 2.4389-2.4918 | 0.2224 | 730 | 0.1834 | 12298 | 13028 | 100 | 2.4918-2.5497 | 0.1903 | 677 | 0.166 | 12360 | 13037 | 100 | 2.5497-2.6133 | 0.1991 | 700 | 0.1698 | 12281 | 12981 | 100 | 2.6133-2.6838 | 0.2235 | 606 | 0.1763 | 12407 | 13013 | 100 | 2.6838-2.7626 | 0.2215 | 677 | 0.1836 | 12374 | 13051 | 100 | 2.7626-2.8515 | 0.2327 | 605 | 0.1735 | 12370 | 12975 | 100 | 2.8515-2.9531 | 0.2227 | 644 | 0.1878 | 12391 | 13035 | 100 | 2.9531-3.0709 | 0.2193 | 724 | 0.1871 | 12217 | 12941 | 99 | 3.0709-3.2102 | 0.2257 | 639 | 0.1947 | 12381 | 13020 | 100 | 3.2102-3.3786 | 0.2229 | 683 | 0.1792 | 12407 | 13090 | 100 | 3.3786-3.5892 | 0.1814 | 613 | 0.1649 | 12348 | 12961 | 100 | 3.5892-3.8645 | 0.1597 | 642 | 0.1472 | 12359 | 13001 | 100 | 3.8645-4.25 | 0.1473 | 639 | 0.1268 | 12388 | 13027 | 100 | 4.25-4.8572 | 0.1556 | 642 | 0.1261 | 12334 | 12976 | 99 | 4.8572-6.0907 | 0.163 | 672 | 0.1464 | 12359 | 13031 | 100 | 6.0907-19.9768 | 0.1829 | 651 | 0.1724 | 12258 | 12909 | 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 | 0.0467 | -0.0252 | -0.0114 | 0.0044 | -0.0034 | -0.0016 | -0.1175 | -0.042 | 0.0422 | 0.0323 | 0.0631 | 0.036 | 0.0722 | -0.07 | -0 | 0.2648 | 0.0183 | -0.0218 | 0.2292 | 0.0016 | 0.17 | 21.0061 | 0.5726 | 60.7211 | 2 | 0.0121 | 0.0002 | -0.0025 | 0.0145 | -0.0052 | -0.0065 | -0.1456 | 0.034 | 0.0018 | 0.0141 | 0.1112 | -0.0001 | -0.0171 | -0.0046 | -0 | 0.2496 | 0.0272 | -0.0686 | 0.2534 | 0.0089 | 0.205 | 24.1155 | 13.2868 | 52.0855 | 3 | 0.0399 | -0.0597 | -0.0474 | 0.0004 | 0.0137 | 0.0221 | -0.1838 | 0.0055 | -0.0637 | -0.0454 | 0.1362 | -0.1121 | -0.0181 | -0.0643 | -0 | 0.3043 | -0.0292 | -0.0544 | 0.2407 | -0.007 | 0.0852 | 31.145 | 1.9107 | 48.1731 | 4 | 0.0324 | -0.072 | -0.0075 | 0.0265 | -0.0002 | 0.0094 | -0.0649 | -0.0138 | -0.0095 | 0.012 | 0.0808 | -0.0078 | 0.0306 | 0.0142 | -0 | 0.2747 | 0.0152 | -0.0514 | 0.226 | -0.0181 | 0.152 | 32.7042 | -4.2259 | 56.0551 | 5 | 0.011 | 0.0131 | -0.0017 | 0.0082 | -0.0005 | 0.0183 | -0.067 | 0.0966 | -0.0876 | -0.0285 | 0.0285 | 0.075 | 0.0303 | -0.0939 | -0 | 0.3453 | -0.0905 | -0.0795 | 0.3873 | -0.0426 | 0.2567 | 11.4159 | -6.8048 | 36.3317 | 6 | 0.0095 | -0.0408 | -0.014 | 0.0007 | 0.0174 | 0.0067 | -0.1488 | 0.0708 | -0.0524 | 0.0283 | 0.0146 | -0.0004 | 0.0985 | 0.0768 | -0 | 0.3154 | -0.0086 | -0.0045 | 0.2223 | -0.0177 | 0.1618 | 30.2546 | -10.9953 | 49.9928 | 7 | 0.0535 | -0.0142 | -0.0224 | 0.0969 | -0.0268 | 0.0181 | -0.1309 | 0.0138 | -0.0248 | 0.0633 | 0.1376 | 0.116 | 0.07 | 0.0187 | 0 | 0.2682 | 0.0245 | 0.0046 | 0.2513 | 0.0182 | 0.1675 | 16.4832 | -3.4106 | 64.0925 | 8 | 0.0342 | 0.0035 | 0.0353 | 0.0162 | 0.0098 | 0.0259 | -0.0569 | -0.0193 | 0.0661 | 0.0015 | -0.0033 | 0.1074 | 0.0382 | -0.082 | -0 | 0.1927 | -0.0826 | 0.0115 | 0.3393 | -0.0125 | 0.2721 | -1.7156 | -1.8754 | 52.7234 | 9 | 0.0012 | 0.0054 | -0.0083 | 0.0234 | 0.0383 | 0.0254 | 0.0105 | 0.0599 | 0.0045 | -0.0231 | 0.0165 | 0.0174 | 0.0171 | 0.0272 | -0 | 0.2368 | 0.0302 | -0.0556 | 0.2895 | 0.0251 | 0.2621 | 19.9434 | 20.8024 | 48.3781 | 10 | 0.0016 | -0.0059 | -0.0084 | 0.0025 | -0.009 | -0.0017 | -0.0214 | -0.0926 | 0.0482 | 0.0401 | -0.0097 | -0.0232 | 0.0104 | -0.0112 | 0 | 0.3545 | 0.0288 | -0.0486 | 0.3093 | -0.0246 | 0.269 | 53.9967 | 6.0985 | 70.7082 | 11 | 0.0079 | -0.0684 | -0.0524 | 0.043 | -0.0299 | 0.1409 | -0.0129 | -0.0461 | 0.0235 | -0.0523 | 0.0882 | 0.0525 | 0.0442 | 0.0686 | -0 | 0.2077 | 0.0137 | 0.0054 | 0.2156 | -0.022 | 0.1907 | 36.1971 | -38.0769 | 90.9197 | 12 | -0.0073 | -0.0279 | -0.0437 | 0.0051 | -0.0198 | 0.0326 | 0.0393 | -0.0536 | -0.1236 | 0.0182 | 0.0965 | 0.0529 | 0.0759 | -0.0792 | -0 | 0.1944 | -0.0013 | -0.0173 | 0.2886 | -0.0052 | 0.1982 | 22.7933 | -35.9838 | 94.7144 | 13 | 0.1072 | 0.045 | -0.0949 | 0.0028 | 0.0065 | 0.0515 | 0.0294 | -0.0193 | 0.0299 | -0.0051 | 0.0806 | 0.0011 | -0.0075 | -0.0639 | 0 | 0.1666 | 0.0326 | -0.0069 | 0.25 | 0.0069 | 0.156 | 24.145 | -28.7031 | 84.3157 | 14 | 0.0401 | -0.0538 | -0.0357 | 0.0057 | -0.079 | 0.2541 | 0.0277 | -0.046 | 0.0259 | -0.0631 | 0.0708 | -0.0281 | -0.0727 | 0.0264 | -0 | 0.1595 | -0.0145 | 0.0196 | 0.2073 | -0.0403 | 0.1683 | 38.495 | -29.2943 | 83.5406 | 15 | -0.0012 | -0.2756 | 0.0922 | 0.1416 | -0.1313 | 0.0413 | 0.0423 | 0.0399 | 0.1116 | -0.0284 | 0.1945 | 0.2622 | 0.1077 | 0.1233 | 0 | 0.1771 | 0.0144 | 0.0635 | 0.0511 | -0.0248 | 0.2014 | 34.5416 | -46.0556 | 89.8089 | 16 | 0.0397 | -0.076 | -0.0528 | 0.059 | 0.0017 | -0.0474 | -0.0131 | 0.0171 | 0.1113 | 0.0201 | 0.0464 | 0.0381 | 0.0846 | 0.0074 | -0 | 0.2059 | 0.053 | -0.0352 | 0.2248 | 0.0017 | 0.3129 | 21.7783 | 40.8616 | 57.7331 | 17 | 0.0335 | -0.0307 | 0.0186 | 0.0172 | 0.0086 | 0 | -0.0299 | -0.0041 | 0.2308 | 0.0075 | 0.1293 | -0.03 | 0.1164 | -0.0447 | -0 | 0.236 | 0.0371 | -0.0319 | 0.282 | -0.0249 | 0.287 | 33.7307 | 43.1849 | 64.7448 | 18 | 0.0179 | 0.0507 | 0.005 | 0.0116 | 0.006 | -0.0022 | 0.0506 | 0.0233 | 0.2112 | -0.0611 | -0.0039 | -0.0034 | 0.0178 | 0.0215 | -0 | 0.2331 | 0.019 | -0.0149 | 0.2768 | -0.021 | 0.3492 | 32.7808 | 49.274 | 56.7575 | 19 | 0.0102 | -0.0168 | -0.0005 | 0.0019 | 0.0001 | -0.0081 | 0.0654 | -0.159 | 0.1858 | 0.0616 | 0.1659 | 0.0011 | 0.0803 | -0.0387 | 0 | 0.3177 | 0.1214 | 0.0259 | 0.3069 | -0.2062 | 0.3814 | 18.213 | 51.6345 | 82.0487 | 20 | 0.01 | -0.0019 | 0.0038 | 0.0022 | -0.0098 | 0.0033 | -0.076 | -0.044 | 0.317 | -0.0454 | -0.086 | 0.0608 | 0.0125 | 0.0498 | 0 | 0.2595 | 0.023 | -0.0187 | 0.2897 | -0.0705 | 0.4323 | 32.2357 | 56.0341 | 63.2696 | 21 | 0.0197 | -0.0504 | -0.0256 | 0.059 | -0.007 | 0.023 | -0.0022 | 0.0242 | 0.1774 | 0.0094 | 0.0269 | 0.1097 | 0.0498 | 0.0389 | -0 | 0.195 | 0.0608 | -0.0165 | 0.2385 | 0.0312 | 0.3805 | 15.0863 | 48.3209 | 53.9131 | 22 | 0.0026 | -0.0296 | -0.0347 | 0.0056 | 0.021 | 0.0284 | 0.0032 | -0.0087 | 0.11 | 0.0825 | 0.0527 | 0.0935 | 0.0773 | 0.0547 | -0 | 0.2183 | 0.0866 | 0.0195 | 0.2459 | -0.0138 | 0.4022 | 0.9041 | 46.773 | 70.2352 | 23 | -0.0067 | -0.0058 | -0.0315 | 0.1588 | 0.0629 | -0.0462 | -0.0326 | -0.0433 | 0.183 | 0.0803 | 0.078 | -0.0165 | -0.0628 | 0.0684 | -0 | 0.2563 | 0.0399 | -0.0239 | 0.2934 | 0.0181 | 0.2892 | 32.8722 | 29.6242 | 55.8708 | 24 | 0.0408 | 0.0414 | 0.0741 | 0.0236 | -0.0056 | 0.0512 | -0.0564 | -0.078 | 0.0129 | -0.1365 | 0.0257 | 0.0206 | 0.0415 | 0.0183 | 0 | 0.3775 | 0.0368 | 0.0835 | 0.219 | 0.0177 | 0.3402 | 33.9142 | -76.2798 | 89.5854 | 25 | -0.0136 | 0.008 | -0.0348 | 0.0076 | -0.0071 | -0.0167 | -0.0361 | -0.0996 | 0.077 | 0.0132 | 0.0285 | 0.0019 | -0.04 | 0.0444 | -0 | 0.3647 | 0.1032 | -0.0343 | 0.4172 | -0.016 | 0.4707 | 50.304 | -71.433 | 101.7943 | 26 | 0.0049 | 0.0395 | 0.0022 | 0.0533 | -0.0454 | -0.0227 | -0.0596 | -0.1453 | 0.0268 | -0.0098 | -0.0199 | 0.1166 | 0.2096 | -0.012 | -0 | 0.3483 | 0.0061 | 0.0814 | 0.2885 | 0.0567 | 0.378 | 27.862 | -81.3557 | 101.6718 | 27 | -0.0246 | 0.0037 | 0.0393 | 0.1181 | -0.094 | -0.0273 | -0.1774 | -0.165 | -0.008 | -0.2371 | -0.0474 | -0.0579 | 0.4438 | -0.0409 | 0 | 0.3646 | 0.1413 | 0.1233 | 0.2144 | 0.075 | 0.4062 | 43.2912 | -86.8794 | 94.4645 | 28 | 0.0177 | 0.0151 | -0.0577 | 0.0597 | -0.012 | -0.0226 | -0.2278 | -0.2143 | 0.034 | -0.247 | 0.0983 | -0.0632 | 0.1639 | -0.0194 | -0 | 0.4619 | 0.0039 | 0.0889 | 0.2269 | -0.0143 | 0.3198 | 39.6241 | -77.454 | 77.2126 | 29 | 0.0115 | -0.0019 | 0.0244 | -0.0056 | 0.0209 | 0.0024 | -0.4037 | 0.1133 | -0.0466 | -0.1617 | 0.1331 | -0.0173 | -0.0363 | 0.0875 | 0 | 0.1443 | 0.4454 | 0.6089 | -0.2026 | -0.43 | 0.137 | 57.3501 | -82.8938 | 74.2653 | 30 | -0.005 | -0.0266 | -0.023 | 0.1134 | -0.0143 | -0.0235 | -0.0994 | -0.0364 | -0.0602 | 0.0908 | 0.0955 | -0.0261 | 0.1002 | -0.0167 | -0 | 0.3522 | 0.0846 | 0.0371 | 0.3392 | -0.0302 | 0.3126 | 29.432 | -63.6648 | 99.6819 |
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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 5 through 101 )A5 - 101 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 102 through 135 )A102 - 135 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 136 through 182 )A136 - 182 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 183 through 214 )A183 - 214 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 215 through 251 )A215 - 251 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 252 through 282 )A252 - 282 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 283 through 378 )A283 - 378 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 379 through 450 )A379 - 450 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 451 through 487 )A451 - 487 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 488 through 512 )A488 - 512 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 5 through 135 )B5 - 135 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 136 through 182 )B136 - 182 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 183 through 251 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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