ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.12_2829精密化 | CrystalClear | | データ収集 | SCALA | | データスケーリング | PDB_EXTRACT | 3.22 | データ抽出 | iMOSFLM | | 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 開始モデル: 6AMJ 解像度: 2.45→33.928 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 22.89 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2354 | 1806 | 4.94 % |
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Rwork | 0.1831 | 34726 | - |
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obs | 0.1857 | 36532 | 98.79 % |
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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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原子変位パラメータ | Biso max: 142.64 Å2 / Biso mean: 37.8094 Å2 / Biso min: 12.21 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.45→33.928 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6408 | 0 | 0 | 538 | 6946 |
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Biso mean | - | - | - | 38.35 | - |
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残基数 | - | - | - | - | 852 |
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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 | 6557 | X-RAY DIFFRACTION | f_angle_d0.564 | 8922 | X-RAY DIFFRACTION | f_chiral_restr0.043 | 1014 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1139 | X-RAY DIFFRACTION | f_dihedral_angle_d9.032 | 3872 | | | | | |
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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: 13 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.45-2.5163 | 0.3256 | 116 | 0.2477 | 2406 | 2522 | 89 | 2.5163-2.5903 | 0.2644 | 132 | 0.2378 | 2666 | 2798 | 98 | 2.5903-2.6738 | 0.2992 | 146 | 0.2353 | 2632 | 2778 | 99 | 2.6738-2.7694 | 0.3152 | 106 | 0.2203 | 2700 | 2806 | 99 | 2.7694-2.8802 | 0.2689 | 150 | 0.2232 | 2695 | 2845 | 99 | 2.8802-3.0112 | 0.269 | 145 | 0.2133 | 2662 | 2807 | 100 | 3.0112-3.1699 | 0.2574 | 139 | 0.2092 | 2675 | 2814 | 100 | 3.1699-3.3683 | 0.3039 | 128 | 0.1987 | 2719 | 2847 | 100 | 3.3683-3.6281 | 0.2402 | 143 | 0.1713 | 2709 | 2852 | 100 | 3.6281-3.9927 | 0.2379 | 149 | 0.1716 | 2680 | 2829 | 100 | 3.9927-4.5692 | 0.1809 | 145 | 0.14 | 2712 | 2857 | 100 | 4.5692-5.7522 | 0.1549 | 127 | 0.139 | 2716 | 2843 | 100 | 5.7522-33.9313 | 0.2074 | 180 | 0.1701 | 2754 | 2934 | 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 | 0.3365 | 0.4999 | 0.7308 | 1.4954 | 0.768 | 3.7492 | -0.0347 | 0.0363 | -0.0062 | -0.3566 | 0.0738 | -0.0131 | -0.0005 | 0.2235 | -0.0905 | 0.3094 | 0.0431 | 0.0242 | 0.2556 | 0.0423 | 0.2478 | 178.3326 | -9.5384 | 129.4268 | 2 | 2.9708 | -0.2952 | 1.983 | 1.1994 | -0.845 | 4.3144 | -0.1493 | 0.0225 | 0.4075 | -0.3241 | 0.0396 | -0.2374 | -0.4273 | 0.3011 | 0.0815 | 0.2764 | -0.043 | 0.043 | 0.2117 | 0.0296 | 0.3133 | 180.5796 | -3.3596 | 131.2366 | 3 | 1.6947 | 2.4176 | -2.3707 | 3.3073 | -3.4148 | 3.4224 | -0.0141 | -0.4509 | -0.1543 | -0.2016 | -0.29 | -0.3947 | 0.0362 | 0.6186 | 0.2111 | 0.1822 | 0.0008 | 0.0417 | 0.3036 | -0.0179 | 0.2691 | 174.3987 | -15.6433 | 149.5326 | 4 | 8.5409 | -3.1762 | 4.1578 | 4.2219 | -2.3635 | 4.0572 | 0.0457 | -0.2204 | 0.539 | 0.1359 | -0.1661 | 0.3046 | 0.2239 | -0.3349 | 0.1813 | 0.2041 | -0.0114 | -0.0007 | 0.2468 | -0.1223 | 0.2632 | 145.3364 | -12.9125 | 156.9449 | 5 | 9.0445 | 0.2579 | 0.6115 | 1.114 | -1.086 | 1.9467 | -0.0622 | -0.2026 | -0.1709 | -0.1781 | 0.0343 | -0.2111 | 0.1735 | 0.1153 | 0.044 | 0.1838 | 0.0246 | -0.0033 | 0.1648 | -0.0404 | 0.1487 | 157.946 | -18.5919 | 150.3813 | 6 | 4.3822 | 1.73 | -0.0914 | 3.7153 | -1.0091 | 0.833 | 0.0324 | 0.5762 | -0.1831 | 0.145 | 0.1412 | -0.1909 | 0.2885 | 0.1626 | -0.1503 | 0.2651 | -0.0178 | -0.0052 | 0.2498 | -0.0733 | 0.1524 | 150.3868 | -20.6248 | 145.3447 | 7 | 7.6004 | 2.9919 | -1.0685 | 2.4608 | -2.5965 | 7.7421 | 0.2631 | -0.4982 | 1.2772 | 0.2555 | 0.3581 | 0.6551 | -0.3104 | 0.4752 | -0.5906 | 0.2602 | 0.0534 | 0.0165 | 0.269 | -0.1057 | 0.335 | 170.3384 | -9.2304 | 152.297 | 8 | 3.2199 | -1.106 | 0.4106 | 3.5005 | -0.5598 | 1.2187 | 0.03 | 0.2895 | -0.31 | -0.104 | 0.0908 | 0.4421 | 0.0518 | -0.1976 | -0.1285 | 0.1784 | -0.0089 | 0.0002 | 0.2152 | -0.0123 | 0.2124 | 145.3736 | -20.3799 | 150.9067 | 9 | 4.3156 | 0.7202 | 1.275 | 3.9412 | -0.3514 | 1.0494 | 0.4432 | -1.152 | -0.8525 | 0.0977 | -0.1885 | -0.0892 | -0.2117 | -0.0033 | -0.0711 | 0.2549 | -0.0258 | 0.048 | 0.1851 | 0.0525 | 0.2577 | 154.3581 | -25.1423 | 157.2443 | 10 | 4.7461 | -0.9722 | -2.8177 | 0.7719 | 0.7365 | 1.8736 | 0.1465 | -0.4962 | 0.3572 | -0.0374 | -0.0501 | -0.1173 | 0.0071 | 0.2818 | 0.0005 | 0.1961 | -0.023 | 0.0186 | 0.2332 | 0.0133 | 0.1941 | 157.0332 | -37.5192 | 155.64 | 11 | 5.5 | -0.559 | -0.9987 | 2.7953 | 0.5386 | 1.9217 | 0.0239 | -0.5157 | -0.5756 | 0.311 | -0.1074 | 0.2183 | 0.1842 | 0.273 | 0.1307 | 0.2349 | -0.0537 | -0.0397 | 0.3058 | 0.0975 | 0.314 | 151.1318 | -46.4036 | 158.1093 | 12 | 5.5628 | -0.6213 | 1.1664 | 4.2715 | -0.5026 | 0.5354 | 0.4401 | -1.3417 | -0.1431 | 1.1271 | -0.6842 | -0.3132 | 0.1624 | 0.2355 | -0.0932 | 0.3345 | -0.0721 | -0.0574 | 0.4768 | 0.1462 | 0.165 | 153.702 | -41.7176 | 164.1977 | 13 | 5.2523 | 0.1365 | -0.5393 | 1.0944 | -0.0268 | 1.4213 | 0.1495 | -0.3946 | -0.3331 | 0.0722 | -0.177 | 0.0713 | 0.0917 | 0.0887 | 0.0222 | 0.208 | 0.0064 | 0.0039 | 0.2635 | 0.0235 | 0.2151 | 151.5327 | -43.9184 | 154.4997 | 14 | 2.9456 | 0.7305 | -1.2606 | 3.0534 | -0.2446 | 0.5671 | -0.4519 | -0.4594 | -0.1459 | 0.1286 | -0.0557 | 0.2011 | 0.3592 | 0.3721 | 0.3791 | 0.2709 | 0.0284 | 0.0236 | 0.4141 | 0.0877 | 0.2196 | 169.9649 | -37.2818 | 145.5804 | 15 | 6.3054 | 0.3324 | 1.7027 | 3.4947 | -0.0797 | 4.1342 | 0.0707 | 0.4807 | -0.0809 | -0.7168 | 0.2338 | 0.2475 | 0.5438 | 0.0321 | -0.4312 | 0.464 | -0.02 | -0.0823 | 0.2715 | -0.0193 | 0.2716 | 163.788 | -29.8263 | 117.0435 | 16 | 2.3889 | -1.2181 | 2.0283 | 2.8853 | -3.5635 | 5.2681 | -0.0435 | -0.1806 | -0.095 | 0.2273 | 0.2404 | 0.3528 | -0.2898 | -0.2976 | -0.1498 | 0.2633 | 0.0369 | 0.0652 | 0.215 | -0.0306 | 0.1974 | 165.4345 | -28.1149 | 132.1778 | 17 | 0.7009 | 0.7459 | -0.141 | 0.929 | 0.5879 | 1.7465 | -0.3127 | 0.11 | 0.0701 | -0.088 | 0.4534 | -0.3724 | 0.1356 | -0.1798 | -0.1111 | 0.2314 | 0.0349 | 0.0349 | 0.2873 | -0.0625 | 0.3062 | 159.2181 | -21.9015 | 128.8115 | 18 | 6.5892 | 1.6468 | 4.2629 | 4.5168 | -3.9843 | 9.3873 | -0.0099 | -0.0751 | -0.2367 | 0.186 | -0.0654 | -0.0462 | -0.0872 | -0.0575 | 0.1105 | 0.3662 | 0.1041 | -0.0499 | 0.1815 | -0.0229 | 0.2333 | 167.8887 | -41.7367 | 139.1403 | 19 | 4.5062 | -0.1618 | 2.1754 | 3.2318 | -2.3524 | 6.2235 | -0.0897 | 0.4527 | 0.3177 | -0.0958 | 0.1278 | 0.1109 | -0.1651 | -0.0065 | -0.0827 | 0.2651 | 0.0127 | 0.0338 | 0.1826 | -0.0053 | 0.2618 | 166.2074 | -21.9888 | 124.1778 | 20 | 4.4062 | 0.1135 | -1.3464 | 2.4874 | 0.122 | 3.8019 | -0.5442 | 0.9004 | -0.5376 | -0.4366 | 0.6409 | 0.1281 | 0.8675 | -0.7527 | -0.2457 | 0.3887 | -0.1421 | -0.0248 | 0.4836 | -0.0335 | 0.3428 | 135.9164 | -54.3323 | 139.9258 | 21 | 4.917 | 0.5769 | -1.8699 | 2.0645 | -1.1837 | 4.6901 | -0.041 | 0.794 | 0.1069 | -0.11 | 0.2373 | 0.3281 | 0.1182 | -0.6029 | -0.1755 | 0.194 | -0.0121 | -0.0266 | 0.3632 | 0.0704 | 0.249 | 134.2747 | -47.6764 | 144.7889 | 22 | 3.6222 | 1.3438 | -3.6655 | 0.5574 | -0.4936 | 7.7153 | -0.1989 | 0.4415 | 0.0611 | 0.0144 | 0.3788 | 0.4096 | -0.2022 | -1.5187 | -0.196 | 0.2568 | -0.0299 | -0.0137 | 0.4306 | -0.0015 | 0.4046 | 142.2771 | -48.5512 | 138.8097 | 23 | 4.1678 | -0.0218 | 0.4446 | 1.3247 | -0.4543 | 3.9314 | 0.0123 | 0.2805 | -0.1094 | -0.1871 | 0.1157 | 0.1267 | 0.3145 | -0.0475 | -0.0523 | 0.308 | -0.0383 | -0.038 | 0.1519 | -0.0373 | 0.2231 | 161.5575 | -39.5565 | 123.1245 | 24 | 3.9801 | 0.2966 | 0.5892 | 2.7822 | -0.2579 | 2.5118 | -0.0876 | 0.697 | -0.1681 | -0.3608 | 0.0877 | 0.1218 | 0.5486 | 0.1439 | 0.0273 | 0.3811 | 0.0057 | -0.0271 | 0.253 | -0.0781 | 0.2058 | 165.921 | -43.1262 | 120.4115 | 25 | 2.8401 | 0.9779 | -0.2167 | 4.4013 | 0.6536 | 5.0421 | 0.1082 | 1.5027 | -0.0854 | -1.179 | 0.0703 | 0.0247 | -0.5323 | 0.0715 | -0.1747 | 0.6136 | -0.0453 | -0.0647 | 0.5447 | -0.0654 | 0.3464 | 163.9354 | -42.1747 | 112.9857 | 26 | 3.22 | 1.6629 | -0.2515 | 4.2216 | -2.014 | 4.4389 | -0.1487 | 0.0745 | 0.3429 | 0.2106 | 0.1018 | -0.4229 | -1.0005 | -0.0454 | 0.0666 | 0.5732 | 0.0431 | -0.1049 | 0.2284 | 0.0668 | 0.6437 | 164.2013 | 14.9824 | 127.9742 | 27 | 3.5512 | -0.9142 | -0.3646 | 2.2236 | -1.1729 | 4.668 | -0.2723 | 0.079 | 0.2111 | -0.2849 | 0.1507 | -0.0282 | -0.2423 | -0.205 | 0.0726 | 0.4131 | 0.0313 | -0.0366 | 0.2364 | 0.0785 | 0.3568 | 163.4155 | 8.1362 | 122.7692 | 28 | 2.7082 | 0.2213 | -1.3425 | 1.3145 | -0.2001 | 1.9963 | 0.0207 | 0.3776 | 0.2609 | 0.1148 | 0.0864 | 0.2044 | -0.2174 | -0.4919 | 0.0316 | 0.22 | 0.0546 | -0.0274 | 0.1823 | -0.0367 | 0.3248 | 153.0767 | -2.1275 | 148.1542 | 29 | 2.6298 | -0.4689 | 0.3 | 1.3452 | -0.6929 | 3.1181 | -0.0011 | -0.014 | 0.4359 | 0.1053 | -0.0602 | -0.2003 | -0.1742 | 0.0026 | 0.0778 | 0.1804 | 0.023 | 0.0019 | 0.2053 | -0.0592 | 0.2874 | 154.3612 | -3.0132 | 156.1232 | 30 | 3.7786 | -1.1396 | 0.9993 | 7.8026 | -1.6299 | 4.9139 | 0.0859 | -0.498 | 0.4876 | 0.7564 | 0.2311 | 0.4679 | -0.8016 | -0.6524 | -0.2105 | 0.3019 | 0.0926 | 0.0392 | 0.4287 | -0.1934 | 0.453 | 146.8587 | -0.2618 | 161.6234 |
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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 'L' and (resid 1 through 38 )L1 - 38 | 2 | X-RAY DIFFRACTION | 2 | chain 'L' and (resid 39 through 102 )L39 - 102 | 3 | X-RAY DIFFRACTION | 3 | chain 'L' and (resid 103 through 113 )L103 - 113 | 4 | X-RAY DIFFRACTION | 4 | chain 'L' and (resid 114 through 128 )L114 - 128 | 5 | X-RAY DIFFRACTION | 5 | chain 'L' and (resid 129 through 150 )L129 - 150 | 6 | X-RAY DIFFRACTION | 6 | chain 'L' and (resid 151 through 163 )L151 - 163 | 7 | X-RAY DIFFRACTION | 7 | chain 'L' and (resid 164 through 174 )L164 - 174 | 8 | X-RAY DIFFRACTION | 8 | chain 'L' and (resid 175 through 197 )L175 - 197 | 9 | X-RAY DIFFRACTION | 9 | chain 'L' and (resid 198 through 214 )L198 - 214 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 1 through 18 )A1 - 18 | 11 | X-RAY DIFFRACTION | 11 | chain 'A' and (resid 19 through 61 )A19 - 61 | 12 | X-RAY DIFFRACTION | 12 | chain 'A' and (resid 62 through 75 )A62 - 75 | 13 | X-RAY DIFFRACTION | 13 | chain 'A' and (resid 76 through 102 )A | | | | | | | | | | | | | | | | | | | | | | | | | |
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