ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | PHENIX | 1.8.2_1309精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | HKL-2000 | | データ収集 | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.42→30.19 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.38 / 位相誤差: 24.89 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.216 | 1543 | 4.31 % |
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Rwork | 0.177 | - | - |
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obs | 0.178 | 35840 | 84.2 % |
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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 mean: 42.12 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.42→30.19 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6719 | 0 | 7 | 173 | 6899 |
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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 | 6894 | X-RAY DIFFRACTION | f_angle_d1.173 | 9364 | X-RAY DIFFRACTION | f_dihedral_angle_d13.696 | 2468 | X-RAY DIFFRACTION | f_chiral_restr0.066 | 1040 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1187 | | | | | |
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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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2.4205-2.4986 | 0.3063 | 71 | 0.2342 | 1555 | X-RAY DIFFRACTION | 43 | 2.4986-2.5878 | 0.3274 | 107 | 0.2352 | 2038 | X-RAY DIFFRACTION | 56 | 2.5878-2.6914 | 0.2914 | 105 | 0.2343 | 2392 | X-RAY DIFFRACTION | 65 | 2.6914-2.8138 | 0.2863 | 126 | 0.2369 | 2798 | X-RAY DIFFRACTION | 76 | 2.8138-2.962 | 0.285 | 142 | 0.2288 | 3364 | X-RAY DIFFRACTION | 90 | 2.962-3.1474 | 0.2838 | 157 | 0.2187 | 3593 | X-RAY DIFFRACTION | 98 | 3.1474-3.3901 | 0.2467 | 168 | 0.1877 | 3701 | X-RAY DIFFRACTION | 100 | 3.3901-3.7307 | 0.213 | 167 | 0.1668 | 3674 | X-RAY DIFFRACTION | 100 | 3.7307-4.2693 | 0.1878 | 168 | 0.154 | 3713 | X-RAY DIFFRACTION | 100 | 4.2693-5.3739 | 0.1531 | 177 | 0.1287 | 3702 | X-RAY DIFFRACTION | 100 | 5.3739-30.1967 | 0.185 | 155 | 0.1728 | 3767 | X-RAY DIFFRACTION | 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 | 0.0063 | -0.0035 | 0.0054 | 0.0007 | 0.0005 | -0.002 | 0.0876 | -0.0245 | 0.0045 | -0.0404 | 0.066 | -0.0129 | -0.0076 | 0.0714 | -0 | 0.1619 | 0.0045 | 0.0082 | 0.1622 | -0.0415 | 0.1988 | 17.9417 | -42.8172 | -1.3373 | 2 | -0.0053 | -0 | 0.0057 | 0.003 | 0.0115 | -0.0101 | 0.0989 | -0.0001 | -0.0424 | -0.0389 | 0.0723 | 0.0157 | 0.0213 | -0.0361 | -0 | -0.5578 | -0.2004 | -0.4904 | -0.369 | -0.2933 | -0.3692 | 12.6065 | -43.1602 | 7.1813 | 3 | -0.069 | 0.0035 | 0.1013 | -0.03 | 0.0331 | -0.0554 | 0.0937 | -0.0765 | -0.0539 | 0.0543 | 0.0833 | 0.0891 | -0.1205 | 0.1005 | 0 | -0.6261 | -0.1912 | -0.7528 | -0.3888 | -0.4106 | -0.8256 | 7.4555 | -37.7557 | -1.1763 | 4 | -0.0036 | -0.0049 | 0.002 | 0.0074 | 0.0052 | 0.0008 | 0.0646 | 0.0129 | 0.0115 | -0.0423 | 0.0522 | -0.0733 | -0.0288 | -0.0298 | 0 | 0.1766 | 0.0609 | -0.0703 | 0.0407 | -0.0811 | 0.2101 | -6.0288 | -51.2545 | -21.809 | 5 | 0.0016 | -0.0024 | 0.002 | 0.0097 | 0.0088 | 0.0016 | 0.0864 | 0.0244 | 0.0014 | 0.0346 | 0.0098 | -0.0488 | 0.0134 | -0.0368 | -0 | 0.1427 | 0.145 | -0.1507 | 0.1162 | -0.0212 | 0.1243 | -10.2172 | -47.8497 | -20.7743 | 6 | -0.0015 | -0.0043 | 0.0043 | 0.0062 | 0.0015 | -0.0029 | 0.0429 | 0.0352 | 0.0003 | -0.0051 | 0.0482 | -0.0551 | -0.0173 | -0.0418 | 0 | 0.1584 | 0.1019 | -0.0396 | 0.0413 | -0.1279 | 0.2284 | -6.5732 | -54.2431 | -29.3223 | 7 | 0.002 | -0.003 | 0.0033 | 0.0039 | 0.0036 | 0.002 | -0.0262 | 0.0194 | -0.0229 | -0.0226 | -0.0205 | 0.0216 | -0.0273 | 0.0358 | 0 | 0.0433 | -0.0335 | 0.0041 | 0.1025 | 0.0006 | 0.1768 | -2.2305 | -21.3884 | -55.9983 | 8 | 0.0046 | 0.0057 | -0.0041 | -0.002 | 0.0014 | -0.0004 | 0.0259 | -0.0037 | -0.0487 | -0.0091 | 0.0218 | -0.0074 | 0.0148 | 0.0226 | -0 | -0.3423 | -0.1013 | -0.0995 | -0.083 | -0.2481 | -0.4189 | -13.6226 | -22.5715 | -56.2831 | 9 | 0.0009 | -0.0007 | 0.0001 | 0.0009 | -0.0011 | 0.0013 | 0.0031 | 0.0249 | 0.0238 | -0.0054 | 0.0048 | 0.0003 | 0.0005 | -0.014 | 0 | 0.1391 | 0.0018 | -0.0045 | 0.1703 | -0.0016 | 0.1921 | -18.2315 | -15.8515 | -63.3475 | 10 | 0.0021 | 0.0233 | 0.0068 | -0.032 | -0.0005 | 0.0029 | 0.1394 | 0.005 | -0.0109 | -0.1482 | 0.0984 | 0.0226 | -0.0832 | -0.0389 | 0 | -0.4125 | -0.0961 | 0.1752 | 0.0673 | -0.0218 | -0.1002 | -16.6129 | -22.799 | -58.5991 | 11 | -0.0041 | 0.0184 | -0.0019 | -0.0228 | 0.0017 | 0.0037 | 0.164 | 0.035 | 0.0395 | -0.0606 | -0.0246 | -0.0233 | -0.1304 | -0.0036 | 0 | -0.254 | -0.2431 | -0.2265 | -0.1112 | -0.2122 | -0.0933 | -1.8096 | -15.7958 | -45.1136 | 12 | 0.01 | 0.0029 | -0.0054 | -0.0027 | 0.0003 | 0.0007 | 0.0008 | -0.0348 | -0.0179 | -0.0222 | -0.0384 | 0.0037 | -0.0095 | 0.0131 | -0 | -0.0849 | -0.0511 | -0.0731 | 0.2528 | 0.003 | 0.0091 | 11.267 | -12.3143 | -34.1794 | 13 | 0.0208 | 0.0016 | -0.01 | -0.0042 | -0.0018 | 0.0048 | 0.0407 | 0.0041 | -0.0026 | 0.032 | 0.0267 | 0.0087 | -0.043 | 0.0529 | -0 | -0.1119 | 0.0291 | -0.0256 | 0.4061 | 0.0337 | 0.0377 | 12.8889 | -12.2654 | -30.8076 | 14 | 0.003 | -0.005 | -0.0064 | -0.0003 | 0.0035 | 0.0037 | -0.0595 | -0.0165 | 0.0115 | -0.0616 | -0.0244 | 0.0754 | -0.0131 | -0.0054 | -0 | 0.0706 | 0.0611 | -0.0029 | 0.1803 | -0.0427 | 0.1035 | -8.0656 | -25.6511 | 1.615 | 15 | 0.0067 | -0.0008 | 0.0028 | 0.004 | -0.0062 | 0.0045 | -0.0182 | 0.088 | -0.0094 | -0.0096 | 0.0014 | -0.01 | -0.0265 | 0.0333 | 0 | 0.1335 | -0.0194 | 0.0896 | -0.0986 | -0.2443 | -0.227 | 2.9938 | -23.3173 | 3.1287 | 16 | 0.001 | 0.0007 | 0.0004 | 0.001 | -0.0012 | 0.0018 | -0.0345 | 0.0119 | 0.0088 | -0.0263 | 0.0348 | 0.0088 | -0.0082 | 0.0009 | 0 | 0.1016 | -0.0145 | -0.0075 | 0.0847 | -0.0102 | 0.0676 | -2.1251 | -18.0898 | 5.7699 | 17 | -0.0013 | -0.0021 | 0.005 | -0.0014 | -0.0036 | -0.0027 | -0.0248 | 0.0354 | -0.0039 | 0.0438 | 0.0003 | 0.0293 | 0.0192 | 0.0071 | -0 | -0.118 | -0.0579 | -0.2502 | -0.0276 | 0.0308 | -0.2981 | 0.6525 | -27.2112 | 1.8069 | 18 | -0 | 0.0024 | 0.0013 | 0.0002 | -0.0009 | 0.0004 | -0.0011 | -0.0078 | 0.0028 | 0.0141 | -0.0131 | 0.0107 | -0.0178 | 0.0151 | -0 | 0.0458 | -0.0899 | -0.0644 | 0.0756 | 0.0159 | 0.0954 | -15.3186 | -28.7548 | -11.7265 | 19 | 0.0031 | 0.003 | -0.0018 | 0.0012 | -0.0011 | 0.0018 | -0.0043 | 0.0003 | -0.0111 | -0.004 | -0.0098 | -0.0074 | -0.0185 | -0.0024 | 0 | 0.1929 | -0.028 | -0.0395 | 0.0947 | -0.1244 | 0.237 | -18.1828 | -57.8795 | -20.1946 | 20 | -0.0051 | 0.0021 | 0.0035 | 0.0012 | 0.0035 | 0.003 | 0.0608 | -0.0105 | -0.023 | -0.0063 | 0.0573 | 0.0061 | -0.0271 | -0.0027 | -0 | 0.2373 | -0.0553 | 0.078 | -0.0768 | -0.1767 | -0.0854 | -20.2529 | -45.0322 | -11.9727 | 21 | -0.0012 | 0.0023 | -0.0009 | -0.0011 | 0.0001 | 0.0008 | -0.0273 | -0.0013 | -0.0083 | 0.0222 | -0.0111 | 0.0202 | -0.0014 | -0.0104 | 0 | 0.2257 | -0.0867 | 0.0297 | 0.2334 | -0.04 | 0.1053 | -21.2297 | -52.5162 | -6.4268 | 22 | -0.001 | 0.008 | 0.0249 | 0.004 | -0.0096 | 0.0004 | -0.0038 | 0.0163 | -0.0484 | 0.0714 | -0.0314 | 0.0814 | 0.0018 | 0.0413 | 0 | 0.2173 | -0.0651 | 0.0303 | -0.0334 | 0.051 | 0.132 | -19.2588 | -49.5318 | -13.4715 | 23 | 0.0036 | 0.0011 | -0.0025 | 0 | 0.0016 | -0.0003 | 0.0885 | 0.0078 | -0.0031 | -0.0021 | 0.054 | 0.0147 | 0.0069 | -0.0279 | -0 | 0.2911 | -0.0422 | 0.1349 | 0.3039 | -0.0785 | 0.4419 | -29.3414 | -47.0496 | -15.2836 | 24 | 0.004 | 0.0008 | -0.0045 | -0.0025 | -0.0035 | -0.0001 | -0.0435 | 0.0169 | 0.0252 | 0.0232 | 0.0055 | 0.0428 | -0.0017 | 0.0132 | -0 | 0.1152 | 0.0282 | -0.0263 | 0.2004 | 0.003 | 0.1322 | -22.9881 | -13.9846 | -34.0229 | 25 | 0.0015 | -0.0013 | -0.0031 | -0 | 0.0026 | 0.0083 | -0.0009 | 0.0216 | 0.0017 | -0.0004 | -0.0081 | -0.016 | 0.0201 | -0.013 | 0 | 0.0245 | 0.0304 | 0.0695 | 0.0646 | -0.072 | 0.0612 | -24.3443 | -19.6001 | -42.036 | 26 | 0.0014 | 0.002 | -0.0001 | 0.0014 | -0.0006 | 0.0016 | 0.0029 | -0.01 | -0.012 | 0.0149 | -0.006 | -0.0205 | 0.0129 | -0.0009 | -0 | 0.0782 | -0.0254 | -0.015 | 0.174 | -0.0301 | 0.0692 | -28.513 | -26.9718 | -38.8768 | 27 | -0.0014 | -0.0048 | -0.0013 | -0.0031 | -0.0026 | 0.0016 | -0.0049 | -0.0092 | -0.0272 | 0.0182 | -0.0309 | -0.037 | 0.018 | 0.0123 | -0 | 0.0862 | -0.0109 | 0.0142 | 0.1158 | 0.0314 | 0.039 | -22.9178 | -23.1928 | -31.0998 | 28 | -0.0001 | -0.0011 | -0 | -0.0038 | -0 | 0.0005 | 0.0322 | 0.0277 | 0.0174 | 0.0198 | -0.0028 | -0.0112 | -0.0097 | -0.0225 | 0 | -0.0248 | 0.0405 | 0.0641 | 0.0026 | -0.0589 | -0.0577 | -23.0129 | -16.5007 | -46.769 | 29 | 0.0008 | 0.0012 | -0.0009 | -0.0017 | 0.0011 | -0 | 0.0145 | -0.0124 | 0.0101 | 0.0068 | 0.0275 | 0.0012 | 0.0079 | -0.0004 | 0 | 0.1162 | -0.0206 | 0.0024 | 0.1282 | -0.0389 | 0.1389 | -12.2967 | -13.3062 | -22.8417 | 30 | -0.0005 | 0.0012 | -0.0057 | 0.0014 | -0.0031 | -0.0076 | 0.0545 | -0.0352 | -0.0155 | 0.012 | 0.0952 | 0.0318 | -0.0633 | 0.023 | -0 | 0.1116 | -0.2337 | 0.2478 | 0.0063 | 0.0354 | 0.1509 | 4.8784 | -0.4988 | -27.4982 | 31 | -0.0007 | 0.0004 | -0.0019 | 0.0002 | 0.0002 | 0.0014 | -0.0135 | -0.0094 | 0.0024 | -0.0104 | -0.0047 | -0.0028 | 0.0277 | -0.0025 | -0 | 0.2204 | 0.0177 | 0.0885 | 0.083 | -0.0226 | 0.1587 | 0.2942 | 6.167 | -32.3463 | 32 | 0.0005 | 0.0001 | -0.0001 | 0.0008 | 0.0002 | 0.0006 | 0.0013 | -0.0008 | 0.0025 | 0.0053 | 0.0164 | -0.0003 | 0.0018 | 0.0154 | -0 | 0.1469 | -0.0044 | 0.0417 | 0.0769 | 0.1078 | 0.0754 | -4.7598 | -16.1804 | -25.0626 | 33 | 0.0005 | -0.0006 | -0.0042 | 0.0011 | 0.0018 | 0.0002 | -0.0223 | -0.0053 | 0.0088 | 0.016 | -0.005 | -0.0082 | 0.0083 | 0.0053 | -0 | 0.2726 | -0.05 | 0.1474 | 0.0759 | -0.0134 | 0.1558 | 9.5355 | 7.1083 | -33.4098 | 34 | 0.0021 | -0.0032 | -0.005 | 0.0035 | 0.0035 | -0.0005 | -0.0027 | -0.0106 | -0.0092 | 0.0153 | 0.0134 | 0.0099 | 0.0114 | 0.001 | 0 | 0.2285 | -0.0471 | 0.2267 | 0.1035 | -0.0077 | 0.2759 | 2.5788 | 7.5284 | -24.2455 | 35 | 0.0009 | -0.0003 | -0.0036 | 0.003 | 0.0053 | -0.0043 | 0.013 | -0.0116 | -0.0104 | 0.0008 | 0.034 | 0.0265 | -0.0177 | 0.0036 | -0 | 0.3609 | -0.0982 | 0.1441 | 0.3028 | -0.1392 | 0.4827 | 1.5637 | 4.8922 | -19.1777 |
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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 H AND RESID 1:32 )H1 - 32 | 2 | X-RAY DIFFRACTION | 2 | ( CHAIN H AND RESID 33:87 )H33 - 87 | 3 | X-RAY DIFFRACTION | 3 | ( CHAIN H AND RESID 88:134 )H88 - 134 | 4 | X-RAY DIFFRACTION | 4 | ( CHAIN H AND RESID 135:157 )H135 - 157 | 5 | X-RAY DIFFRACTION | 5 | ( CHAIN H AND RESID 158:189 )H158 - 189 | 6 | X-RAY DIFFRACTION | 6 | ( CHAIN H AND RESID 190:214 )H190 - 214 | 7 | X-RAY DIFFRACTION | 7 | ( CHAIN A AND RESID 1:17 )A1 - 17 | 8 | X-RAY DIFFRACTION | 8 | ( CHAIN A AND RESID 18:52 )A18 - 52 | 9 | X-RAY DIFFRACTION | 9 | ( CHAIN A AND RESID 53:66 )A53 - 66 | 10 | X-RAY DIFFRACTION | 10 | ( CHAIN A AND RESID 67:100 )A67 - 100 | 11 | X-RAY DIFFRACTION | 11 | ( CHAIN A AND RESID 101:134 )A101 - 134 | 12 | X-RAY DIFFRACTION | 12 | ( CHAIN A AND RESID 135:157 )A135 - 157 | 13 | X-RAY DIFFRACTION | 13 | ( CHAIN A AND RESID 158:214 )A158 - 214 | 14 | X-RAY DIFFRACTION | 14 | ( CHAIN L AND RESID 1:18 )L1 - 18 | 15 | X-RAY DIFFRACTION | 15 | ( CHAIN L AND | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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