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 | | PHASER | 2.1.4位相決定 | | PHENIX | 1.7.3_928精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | Blu-Ice | | データ収集 | | DENZO | | データ削減 | | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.201→19.853 Å / Occupancy max: 1 / Occupancy min: 0.65 / SU ML: 0.23 / σ(F): 0 / 位相誤差: 22.34 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2154 | 1645 | 5.08 % | random |
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Rwork | 0.1763 | - | - | - |
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obs | 0.1783 | 32403 | 95.4 % | - |
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all | - | 32403 | - | - |
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溶媒の処理 | 減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 33.118 Å2 / ksol: 0.341 e/Å3 |
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原子変位パラメータ | Biso max: 142.77 Å2 / Biso mean: 38.175 Å2 / Biso min: 4.26 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.9515 Å2 | 0 Å2 | 1.2053 Å2 |
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2- | - | 1.3344 Å2 | 0 Å2 |
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3- | - | - | 0.1235 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.201→19.853 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5014 | 0 | 30 | 189 | 5233 |
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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_d0.009 | 5154 | X-RAY DIFFRACTION | f_angle_d1.174 | 6970 | X-RAY DIFFRACTION | f_chiral_restr0.08 | 754 | X-RAY DIFFRACTION | f_plane_restr0.006 | 912 | X-RAY DIFFRACTION | f_dihedral_angle_d15.543 | 1906 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | タイプ | Rms dev position (Å) |
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1 | 1 | A2328 | X-RAY DIFFRACTION | POSITIONAL0.019 | 1 | 2 | B2328 | X-RAY DIFFRACTION | POSITIONAL0.019 | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.2014-2.2661 | 0.3174 | 76 | 0.224 | 1625 | 1701 | 60 | 2.2661-2.3391 | 0.2548 | 137 | 0.2333 | 2314 | 2451 | 88 | 2.3391-2.4226 | 0.303 | 140 | 0.2167 | 2627 | 2767 | 99 | 2.4226-2.5194 | 0.238 | 138 | 0.1983 | 2704 | 2842 | 100 | 2.5194-2.6338 | 0.2072 | 154 | 0.1846 | 2683 | 2837 | 100 | 2.6338-2.7723 | 0.2475 | 145 | 0.1862 | 2669 | 2814 | 100 | 2.7723-2.9455 | 0.2527 | 145 | 0.1915 | 2682 | 2827 | 100 | 2.9455-3.172 | 0.2325 | 150 | 0.1874 | 2669 | 2819 | 100 | 3.172-3.4897 | 0.2219 | 137 | 0.1855 | 2697 | 2834 | 100 | 3.4897-3.9911 | 0.1932 | 142 | 0.1675 | 2696 | 2838 | 100 | 3.9911-5.0149 | 0.1661 | 139 | 0.1355 | 2688 | 2827 | 100 | 5.0149-19.8541 | 0.1866 | 142 | 0.1608 | 2704 | 2846 | 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 | 0.0023 | -0.0028 | 0.0038 | 0.0055 | -0.0009 | 0.0074 | -0.0097 | -0.0156 | -0.0043 | 0.0167 | -0.0076 | -0.0134 | 0.0024 | 0.0142 | -0.0323 | 0.0753 | 0.0586 | -0.0367 | 0.2601 | 0.1743 | 0.0162 | 16.5915 | 25.8121 | 22.0843 | 2 | 0.041 | 0.0415 | -0.0234 | 0.0387 | -0.018 | 0.0631 | -0.0598 | -0.0589 | -0.0551 | 0.0296 | -0.0384 | -0.0222 | 0.0286 | 0.0384 | -0.2005 | 0.1507 | 0.0967 | 0.005 | -0.0144 | 0.1571 | 0.1167 | 6.2927 | 24.787 | -0.7481 | 3 | 0.0193 | 0.0136 | 0.0087 | 0.0112 | 0.0036 | 0.0084 | -0.002 | 0.0025 | -0.0129 | 0.0015 | -0.0005 | 0.0053 | 0.0113 | -0.0117 | -0.0017 | 0.2415 | -0.1616 | 0.0568 | 0.2357 | 0.0272 | 0.2661 | -4.3895 | 21.9121 | 4.5665 | 4 | 0.0005 | 0.0005 | -0.0007 | 0.0019 | 0.0015 | 0.0043 | -0.0037 | -0.01 | -0.0157 | 0.0165 | -0.0227 | -0.0001 | 0.0355 | 0 | -0.0463 | 0.3083 | -0.1315 | 0.0763 | 0.1318 | 0.2149 | 0.3073 | 5.2893 | 12.9213 | 12.175 | 5 | 0.0597 | 0.0467 | -0.0769 | 0.0346 | -0.0587 | 0.097 | -0.0487 | -0.0692 | -0.048 | -0.0357 | -0.0033 | -0.0018 | -0.008 | 0.0343 | -0.0919 | 0.1191 | 0.0552 | 0.0153 | 0.035 | 0.1556 | 0.0233 | 10.1408 | 25.9348 | 8.6432 | 6 | 0.02 | -0.0113 | 0.0001 | 0.0465 | -0.0345 | 0.0295 | -0.0001 | -0.0116 | -0.0117 | 0.0041 | 0.0028 | 0.0096 | -0.0007 | -0.0036 | 0.011 | 0.2117 | -0.0026 | 0.1462 | 0.2905 | 0.0903 | 0.2064 | 1.6635 | 23.6988 | 16.7268 | 7 | 0.0454 | -0.009 | 0.0161 | 0.0131 | 0.0154 | 0.0347 | -0.0074 | -0.0542 | -0.0549 | 0.0424 | 0.0058 | 0.0161 | 0.062 | 0 | 0.0049 | 0.1001 | -0.0172 | 0.062 | 0.1301 | 0.112 | 0.0639 | 12.908 | 31.4381 | 4.1521 | 8 | 0.0006 | 0.0008 | 0.0014 | 0.0008 | 0.0016 | 0.003 | -0.0059 | 0.0138 | -0.0076 | -0.0037 | -0.01 | 0.0003 | -0.0021 | 0.0057 | -0.0001 | 0.3202 | -0.0018 | 0.0357 | 0.274 | 0.048 | 0.2994 | 15.9347 | 47.7391 | -7.2602 | 9 | 0.0453 | 0.0017 | -0.0067 | 0.0129 | -0.0014 | 0.001 | -0.0029 | -0.051 | 0.0398 | 0.0106 | 0.0064 | -0.0176 | -0.0343 | 0.0196 | 0.0119 | 0.0736 | -0.0396 | -0.0034 | 0.0996 | -0.0433 | 0.0936 | 17.3908 | 44.1687 | 5.7748 | 10 | 0.0049 | -0.0062 | 0.0076 | 0.0063 | -0.0089 | 0.0097 | 0.0059 | -0.0217 | -0.0061 | -0.0031 | 0.0096 | 0.0124 | -0.0074 | -0.0371 | 0.0395 | -0.0078 | 0.0306 | 0.0131 | 0.1551 | 0.0062 | -0.03 | 13.839 | 34.4465 | 8.9251 | 11 | 0.0005 | -0.0017 | -0.0006 | 0.011 | 0.0059 | 0.0047 | 0.0059 | 0.0088 | 0.0147 | -0.004 | -0.0028 | 0.0008 | 0 | 0.0054 | 0 | 0.1717 | 0.0658 | 0.0628 | 0.2132 | 0.0093 | 0.1553 | 26.6557 | 33.4861 | -9.812 | 12 | 0.0098 | 0.0071 | 0.013 | 0.0257 | 0.0103 | 0.0221 | -0.0328 | -0.0126 | 0.0514 | -0.0201 | -0.0046 | 0.0065 | -0.0149 | 0.0131 | -0.0209 | -0.0189 | -0.048 | -0.0489 | 0.2159 | -0.0339 | 0.0977 | 24.3514 | 38.5188 | 4.8686 | 13 | 0.0393 | 0.0302 | 0.011 | 0.0244 | 0.0071 | 0.0418 | 0.006 | -0.0418 | -0.069 | -0.0296 | -0.0108 | -0.0003 | 0.0428 | 0.0447 | -0.0518 | -0.029 | 0.1525 | -0.0619 | 0.1971 | 0.0856 | 0.0945 | 30.2485 | 26.0215 | 0.4874 | 14 | 0.0172 | -0.0324 | -0.0035 | 0.0614 | 0.0186 | 0.0203 | -0.0229 | 0.0015 | -0.0375 | -0.0162 | -0.0336 | 0.022 | 0.0425 | 0.0449 | -0.1569 | 0.0885 | 0.1739 | 0.0083 | 0.1797 | 0.164 | 0.2376 | 26.3546 | 18.4854 | 0.0234 | 15 | 0.0019 | 0.0034 | -0.0029 | 0.0111 | -0.008 | 0.0061 | -0.0031 | 0.0049 | -0.0097 | -0.0014 | -0.0045 | -0.0131 | 0.0101 | 0.0027 | -0.0011 | 0.4024 | 0.1822 | 0.0715 | 0.2136 | 0.0066 | 0.5154 | 26.9921 | 8.1274 | -2.8574 | 16 | 0.0436 | -0.0256 | 0.0227 | 0.0147 | -0.0125 | 0.0128 | 0.0166 | -0.0008 | -0.0267 | 0.0107 | 0.0036 | -0.0027 | 0.0025 | 0.0104 | 0.0152 | 0.2382 | 0.2588 | -0.091 | 0.3129 | 0.1951 | 0.3782 | 34.0616 | 13.529 | 8.0598 | 17 | 0.0364 | -0.0131 | -0.0095 | 0.0186 | 0.0062 | 0.0019 | -0.0385 | 0.0145 | -0.0612 | 0.0114 | -0.0405 | -0.037 | 0.0271 | 0.0286 | -0.1297 | 0.1753 | -0.0453 | 0.0405 | -0.0318 | 0.0519 | 0.2244 | 8.081 | 16.0992 | -4.3003 | 18 | 0.0063 | -0.0068 | -0.0023 | 0.0173 | -0.0003 | 0.0022 | 0.0023 | -0.0021 | -0.027 | -0.0186 | -0.021 | 0.0279 | 0.0086 | 0.0088 | -0.0289 | 0.3974 | 0.0217 | 0.0532 | 0.0683 | 0.095 | 0.5622 | 16.1487 | 6.8809 | 2.5007 | 19 | 0.0011 | -0.0013 | 0.0011 | 0.0029 | 0.0029 | 0.0093 | -0.0105 | -0.0016 | -0.0107 | 0.0014 | -0.0212 | -0.0061 | 0.0059 | 0.0007 | -0 | 0.5896 | 0.2095 | -0.1089 | 0.4205 | 0.1512 | 0.6046 | 29.9289 | 2.7832 | 12.9796 | 20 | 0.0042 | -0.0071 | 0.0039 | 0.0138 | -0.0093 | 0.0052 | -0.0096 | -0.0175 | -0.022 | 0.0075 | -0.0101 | -0.0161 | 0.0314 | 0.0219 | -0.0322 | 0.1919 | 0.1162 | -0.0111 | 0.3315 | 0.2922 | 0.2216 | 26.1342 | 17.7301 | 16.3345 | 21 | 0.0112 | -0.0065 | -0.0031 | 0.0159 | 0.0031 | 0.0003 | 0.0093 | 0.0036 | 0.0028 | -0.0142 | -0.0042 | 0.0301 | -0.0034 | -0.0148 | -0.0022 | 0.0261 | 0.1363 | -0.0584 | 0.2883 | 0.0916 | 0.0931 | -20.304 | 44.3726 | -18.8243 | 22 | 0.0366 | -0.0044 | 0.0002 | 0.0111 | 0.0193 | 0.0277 | 0.0497 | 0.02 | 0.0286 | -0.0129 | -0.001 | 0.0134 | -0.0465 | -0.0493 | 0.0678 | 0.0878 | 0.1654 | 0.0061 | -0.072 | 0.1033 | 0.1145 | 1.3528 | 45.4114 | -6.2427 | 23 | 0.0031 | 0.0064 | 0.0061 | 0.017 | 0.0052 | 0.023 | 0.0072 | -0.0123 | 0.0094 | 0.0068 | 0.0021 | 0.0082 | -0.0147 | 0.0016 | 0.0054 | 0.2925 | 0.0611 | 0.0522 | 0.2405 | -0.1605 | 0.2468 | -5.0278 | 48.302 | 3.8354 | 24 | 0.0039 | -0.002 | -0.0007 | 0.0033 | -0.0022 | 0.0044 | 0.0048 | -0.0103 | 0.0183 | -0.0008 | -0.0053 | 0.0145 | -0.0183 | -0.0037 | -0.0043 | 0.3246 | 0.2238 | 0.0642 | 0.1423 | -0.1074 | 0.3618 | -11.607 | 57.282 | -6.5787 | 25 | 0.0983 | -0.0481 | -0.0703 | 0.0469 | 0.0324 | 0.0513 | 0.0271 | 0.0221 | 0.0042 | 0.0084 | 0.0098 | -0.0124 | -0.0561 | -0.0828 | 0.0869 | 0.0005 | 0.172 | -0.0403 | 0.0089 | 0.0644 | 0.0808 | -7.592 | 44.2605 | -11.0287 | 26 | 0.0235 | -0.0218 | 0.0056 | 0.0253 | -0.0132 | 0.0132 | 0 | -0.0056 | -0.0001 | 0.0094 | 0.0009 | 0.0056 | -0.0127 | -0.0103 | -0.0001 | 0.1443 | 0.077 | 0.1238 | 0.2464 | 0.0009 | 0.1738 | -16.5051 | 46.5017 | -3.4278 | 27 | 0.0343 | 0.002 | 0.0217 | 0.0246 | -0.0196 | 0.0404 | -0.001 | 0.0094 | 0.0961 | 0.003 | -0.0015 | 0.0398 | -0.0701 | -0.0545 | -0.0057 | 0.0733 | 0.1006 | 0.0299 | 0.1082 | 0.0115 | 0.1202 | -2.8373 | 38.7532 | -13.3252 | 28 | 0.0085 | 0.0018 | -0.0034 | 0.0007 | -0.0016 | 0.0046 | 0.0077 | 0.0013 | -0.0058 | 0.0034 | -0.0026 | -0.0054 | -0.0026 | 0.0131 | 0 | 0.2803 | 0.0365 | 0.0579 | 0.2813 | -0.016 | 0.3478 | 8.8216 | 22.4552 | -15.1445 | 29 | 0.0002 | 0.0001 | -0.0001 | 0.0109 | -0.0135 | 0.0264 | -0.0078 | 0.0249 | -0.0323 | -0.0333 | -0.001 | 0.0011 | 0.0255 | -0.045 | -0.0104 | 0.1059 | -0.0358 | -0.0025 | 0.0989 | -0.06 | 0.0805 | -3.9972 | 26.0245 | -17.9329 | 30 | 0.0088 | -0.0095 | 0.0052 | 0.0098 | -0.0082 | 0.0075 | -0.0088 | -0.0358 | -0.008 | 0.0108 | -0.0086 | 0.0044 | -0.0046 | -0.0395 | -0.0441 | -0.0152 | 0.0142 | 0.0255 | 0.188 | 0.0251 | 0.0077 | -7.4977 | 35.747 | -14.7291 | 31 | 0.0041 | 0.0049 | 0.0012 | 0.0108 | 0.0016 | 0.0014 | -0.0202 | 0.0064 | -0.0072 | 0.0028 | -0.0158 | -0.0023 | 0.0241 | 0.0049 | -0.0001 | 0.1183 | 0.0094 | 0.0731 | 0.2152 | 0.0592 | 0.2001 | 12.4535 | 36.7002 | -25.5614 | 32 | 0.0105 | 0.0038 | 0.0096 | 0.0106 | 0.0023 | 0.0115 | 0.0118 | 0.0167 | -0.0017 | 0.0006 | 0.0019 | -0.0169 | 0.0361 | -0.019 | -0.001 | 0.1046 | -0.0134 | -0.0234 | 0.2084 | -0.05 | -0.0357 | -2.385 | 31.668 | -24.7681 | 33 | 0.0376 | -0.0039 | 0.0099 | 0.0142 | 0.0157 | 0.0268 | -0.0002 | 0.0612 | 0.0332 | -0.0029 | -0.0126 | -0.0241 | -0.0375 | -0.0227 | -0.0162 | 0.098 | 0.0624 | -0.0383 | 0.2002 | 0.1782 | -0.0384 | 2.5746 | 44.1585 | -30.1981 | 34 | 0.0087 | -0.0023 | 0.0062 | 0.0177 | -0.0119 | 0.0091 | 0.0141 | 0.0369 | 0.0512 | 0.0276 | -0.0058 | -0.0088 | -0.0317 | -0.0041 | 0.0884 | 0.2379 | 0.1549 | 0.0089 | 0.1914 | 0.192 | 0.1123 | 2.6276 | 51.705 | -26.3241 | 35 | 0.002 | -0.0014 | 0.001 | 0.0112 | -0.0023 | 0.0016 | 0.0015 | 0.004 | 0.0067 | -0.0155 | -0.0029 | -0.0038 | -0.0078 | 0.0034 | -0.0049 | 0.4668 | 0.014 | 0.0911 | 0.2164 | 0.191 | 0.3829 | 5.5659 | 62.0538 | -26.6353 | 36 | 0.0027 | -0.0043 | 0.0075 | 0.0088 | -0.0156 | 0.027 | -0.0063 | 0.0123 | -0.0008 | 0.0001 | -0.0012 | 0.0128 | -0.025 | -0.0005 | -0.0048 | 0.3436 | 0.17 | -0.0539 | 0.2735 | 0.2882 | 0.2132 | -4.5762 | 56.6439 | -34.7805 | 37 | 0.0011 | -0.0014 | -0.0092 | 0.0182 | -0.0051 | 0.0402 | 0.0302 | 0.0154 | 0.0397 | -0.0184 | -0.0082 | -0.0078 | -0.0492 | 0.0172 | 0.0412 | 0.23 | 0.058 | 0.0455 | -0.0487 | -0.0202 | 0.2304 | 5.0913 | 54.116 | -7.6362 | 38 | 0.0026 | -0.0067 | 0.0051 | 0.0132 | -0.0098 | 0.0081 | -0.0021 | 0.0083 | 0.0231 | 0.0089 | -0.0175 | -0.0009 | -0.0327 | -0.0002 | -0.0051 | 0.4682 | 0.0918 | 0.0622 | 0.0322 | 0.021 | 0.4119 | -0.8812 | 63.3402 | -16.4056 | 39 | 0.0008 | -0.0011 | 0.0006 | 0.0015 | -0.0011 | 0.0006 | 0.0141 | -0.0034 | 0.0071 | -0.0014 | -0.0004 | -0.0011 | -0.0073 | 0.0021 | -0 | 0.6318 | 0.1595 | -0.0623 | 0.3903 | 0.2151 | 0.5716 | -9.8906 | 67.3922 | -31.1823 | 40 | 0.0029 | -0.0058 | 0.0036 | 0.01 | -0.0066 | 0.0034 | 0.0125 | 0.0136 | 0.0293 | -0.0116 | -0.0007 | 0.0045 | -0.0133 | -0.0178 | 0.0147 | 0.2019 | 0.2382 | -0.0142 | 0.2963 | 0.1252 | 0.2067 | -13.6129 | 52.4498 | -27.7333 |
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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 3:19)A3 - 19 | 2 | X-RAY DIFFRACTION | 2 | (chain A and resid 20:41)A20 - 41 | 3 | X-RAY DIFFRACTION | 3 | (chain A and resid 42:47)A42 - 47 | 4 | X-RAY DIFFRACTION | 4 | (chain A and resid 48:61)A48 - 61 | 5 | X-RAY DIFFRACTION | 5 | (chain A and resid 62:81)A62 - 81 | 6 | X-RAY DIFFRACTION | 6 | (chain A and resid 82:87)A82 - 87 | 7 | X-RAY DIFFRACTION | 7 | (chain A and resid 88:109)A88 - 109 | 8 | X-RAY DIFFRACTION | 8 | (chain A and resid 110:114)A110 - 114 | 9 | X-RAY DIFFRACTION | 9 | (chain A and resid 115:131)A115 - 131 | 10 | X-RAY DIFFRACTION | 10 | (chain A and resid 132:149)A132 - 149 | 11 | X-RAY DIFFRACTION | 11 | (chain A and resid 150:155)A150 - 155 | 12 | X-RAY DIFFRACTION | 12 | (chain A and resid 156:175)A156 - 175 | 13 | X-RAY DIFFRACTION | 13 | (chain A and resid 176:217)A176 - 217 | 14 | X-RAY DIFFRACTION | 14 | (chain A and resid 218:240)A218 - 240 | 15 | X-RAY DIFFRACTION | 15 | (chain A and | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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