ソフトウェア | 名称 | バージョン | 分類 |
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BLU-MAX | | データ収集 | PHENIX | | モデル構築 | BUSTER | 2.10.0精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | PHENIX | | 位相決定 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.28→29.48 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.297 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.212 | 1989 | 4.12 % | RANDOM |
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Rwork | 0.173 | - | - | - |
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obs | 0.174 | 48301 | 96 % | - |
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all | - | 48301 | - | - |
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原子変位パラメータ | Biso mean: 47.17 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 7.5136 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -2.8514 Å2 | 0 Å2 |
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3- | - | - | -4.6621 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.26 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.28→29.48 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 7678 | 0 | 59 | 554 | 8291 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 | Restraint function | Weight |
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X-RAY DIFFRACTION | t_bond_d0.01 | 7901 | HARMONIC2 | X-RAY DIFFRACTION | t_angle_deg1.06 | 10638 | HARMONIC2 | X-RAY DIFFRACTION | t_dihedral_angle_d | 3730 | SINUSOIDAL2 | X-RAY DIFFRACTION | t_incorr_chiral_ct | | | | X-RAY DIFFRACTION | t_pseud_angle | | | | X-RAY DIFFRACTION | t_trig_c_planes | 229 | HARMONIC2 | X-RAY DIFFRACTION | t_gen_planes | 1131 | HARMONIC5 | X-RAY DIFFRACTION | t_it | 7901 | HARMONIC20 | X-RAY DIFFRACTION | t_nbd | | | | X-RAY DIFFRACTION | t_omega_torsion3.19 | | | | X-RAY DIFFRACTION | t_other_torsion2.85 | | | | X-RAY DIFFRACTION | t_improper_torsion | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion | 1026 | SEMIHARMONIC5 | X-RAY DIFFRACTION | t_sum_occupancies | | | | X-RAY DIFFRACTION | t_utility_distance | | | | X-RAY DIFFRACTION | t_utility_angle | | | | X-RAY DIFFRACTION | t_utility_torsion | | | | X-RAY DIFFRACTION | t_ideal_dist_contact | 9305 | SEMIHARMONIC4 | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.28→2.34 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2154 | 103 | 4.37 % |
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Rwork | 0.1886 | 2254 | - |
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all | 0.1898 | 2357 | - |
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obs | - | - | 96 % |
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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 | 2.8881 | -0.7361 | -0.6772 | 3.2676 | -0.1585 | 2.5746 | 0.083 | 0.5038 | -0.0595 | -0.1978 | -0.0956 | -0.0092 | 0.0091 | 0.1474 | 0.0126 | -0.0695 | 0.0528 | -0.0184 | 0.021 | -0.022 | -0.0887 | 46.394 | 20.3892 | -26.0072 | 2 | 1.8557 | -1.9109 | 0.8608 | 3.3735 | -1.6722 | 4.0368 | 0.0368 | 0.424 | -0.0199 | -0.17 | -0.0341 | 0.1554 | -0.0371 | -0.0436 | -0.0027 | -0.052 | 0.0616 | 0.0022 | 0.0577 | -0.0749 | -0.0397 | 43.6882 | 16.7507 | -27.351 | 3 | 3.1907 | -1.331 | -1.1408 | 1.1649 | 0.2737 | 1.1442 | -0.0139 | 0.3593 | 0.0514 | 0.0303 | -0.0043 | 0.0087 | -0.1042 | -0.1195 | 0.0182 | 0.0069 | 0.0344 | -0.0026 | -0.0067 | -0.0135 | -0.028 | 35.9597 | 24.2291 | -13.3266 | 4 | 2.3173 | -0.2683 | -1.1299 | 0.6384 | 0.2067 | 1.4174 | 0.0173 | -0.0798 | 0.0781 | 0.0111 | -0.0232 | -0.0785 | -0.031 | 0.105 | 0.0059 | 0.0007 | 0.0067 | -0.0149 | -0.0705 | -0.0349 | -0.0392 | 41.5091 | 26.9197 | -7.2467 | 5 | 1.3379 | -0.1448 | -1.0897 | 1.5273 | 0.895 | 0.7647 | 0.176 | 0.0004 | -0.0042 | -0.102 | -0.0148 | -0.2564 | 0.0143 | 0.1734 | -0.1612 | -0.0454 | -0.0068 | 0.0271 | -0.001 | -0.0211 | -0.068 | 45.6569 | 43.2953 | 5.2815 | 6 | 3.3671 | -0.9091 | -0.7289 | 2.7471 | 0.351 | 2.2274 | 0.1737 | -0.0967 | 0.4836 | -0.1029 | -0.047 | -0.1912 | -0.2855 | 0.3258 | -0.1267 | -0.0405 | -0.0305 | 0.0618 | -0.0757 | -0.0324 | -0.0515 | 41.1152 | 62.9573 | 9.4899 | 7 | 0.5419 | -0.357 | 0.4012 | 1.6186 | 0.312 | 1.6314 | 0.0635 | 0.1911 | 0.0985 | -0.2799 | -0.0401 | 0.0567 | -0.046 | 0.129 | -0.0235 | -0.0464 | 0.0601 | 0.0466 | 0.0145 | 0.0093 | -0.0473 | 39.0943 | 50.6316 | 4.6933 | 8 | 0 | -0.8951 | -0.633 | 2.3161 | 1.1275 | 0.9089 | 0.1168 | -0.0268 | 0.0429 | -0.1234 | -0.2853 | 0.0056 | -0.1098 | -0.2116 | 0.1685 | -0.0388 | 0.0277 | -0.0163 | -0.0119 | -0.0601 | 0.0055 | 19.6347 | 48.6766 | 15.0592 | 9 | 1.2644 | 1.3824 | 3.0305 | 1.9213 | -0.8994 | 3.0621 | -0.0061 | 0.1675 | 0.0618 | -0.1095 | 0.0282 | 0.059 | -0.0229 | -0.0791 | -0.0221 | 0.1139 | 0.0897 | 0.0569 | 0.0608 | -0.0163 | 0.0074 | 17.8134 | 67.3044 | 15.1258 | 10 | 4.7642 | 0.4821 | -1.4916 | 5.1056 | 1.1363 | 3.1541 | 0.0535 | -0.3983 | 0.0057 | 0.2891 | 0.0048 | -0.3511 | -0.0663 | -0.0646 | -0.0583 | -0.0717 | 0.0012 | 0.0328 | -0.0817 | -0.0651 | -0.0513 | 30.318 | 59.8708 | 25.0511 | 11 | 3.4312 | -1.0198 | -1.3706 | 1.9865 | 0.3653 | 2.8624 | -0.0532 | -0.1982 | -0.0888 | 0.121 | -0.0377 | -0.1621 | 0.0625 | -0.1101 | 0.0909 | -0.0041 | 0.0438 | 0.0476 | -0.062 | -0.0937 | -0.0498 | 19.698 | 59.7571 | 29.1295 | 12 | 0.1959 | -1.6341 | -0.7429 | 3.5947 | 2.1977 | 1.7614 | -0.023 | -0.0464 | -0.0962 | 0.2513 | -0.1456 | 0.0821 | 0.0307 | -0.2597 | 0.1686 | -0.0522 | 0.0506 | 0.0411 | 0.0236 | -0.0792 | 0.0012 | 14.6582 | 56.8048 | 27.1511 | 13 | 2.4023 | 0.1976 | 0.9232 | 1.7033 | 0.3293 | 2.347 | 0.2082 | -0.1945 | -0.5659 | 0.1103 | -0.0202 | -0.0666 | 0.4703 | -0.1238 | -0.188 | -0.0691 | -0.0029 | -0.0416 | -0.0689 | -0.0174 | -0.0155 | 25.0729 | -1.7313 | -3.392 | 14 | 2.7685 | 3.2209 | -1.4026 | 1.8615 | -0.8417 | 0 | -0.0192 | 0.2642 | -0.024 | -0.1615 | 0.0232 | -0.1593 | 0.1857 | 0.0995 | -0.0041 | -0.0323 | 0.0295 | -0.0029 | 0.0632 | -0.1178 | -0.0441 | 26.3028 | 4.1595 | -15.0095 | 15 | 3.6723 | 0.4591 | 1.167 | 0 | -1.6154 | 0.2643 | 0.0229 | 0.232 | -0.3015 | -0.1284 | 0.0199 | -0.0421 | 0.0918 | -0.1502 | -0.0428 | -0.0821 | -0.0166 | -0.0206 | -0.0089 | -0.0574 | 0.0094 | 23.9243 | 1.7827 | -11.1019 | 16 | 4.9601 | 0.5317 | 0.7121 | 0.7714 | 0.0592 | 1.8652 | -0.0567 | -0.1724 | -0.3018 | 0.0702 | -0.0819 | -0.1235 | -0.061 | -0.0834 | 0.1386 | -0.0028 | -0.0089 | 0.0023 | -0.064 | 0.0015 | 0.015 | 33.9642 | 12.2986 | -4.907 | 17 | 1.322 | -2.3226 | -0.0124 | 1.1559 | -1.8577 | 0.0014 | 0.0075 | -0.369 | 0.0973 | 0.0819 | 0.1362 | 0.0468 | 0.0358 | -0.1232 | -0.1437 | -0.0415 | -0.0396 | 0.0093 | 0.1386 | -0.0484 | -0.026 | 16.6188 | 8.5181 | 4.2969 | 18 | 3.8757 | 0.9341 | 0.6977 | 0.8196 | 0.1899 | 0.3263 | -0.0225 | -0.4344 | -0.1136 | 0.0276 | -0.0596 | 0.0107 | -0.0261 | -0.1068 | 0.0821 | -0.0019 | 0.0119 | 0.0053 | -0.0196 | -0.0244 | -0.0353 | 35.3321 | 21.529 | 0.8116 | 19 | 2.1436 | 3.1182 | -0.145 | 0.4135 | -1.017 | 2.4969 | 0.1294 | -0.3146 | -0.2321 | 0.0565 | -0.1839 | -0.2774 | 0.2902 | 0.0242 | 0.0545 | 0.0094 | -0.0305 | 0.0155 | -0.0226 | 0.003 | -0.0661 | 26.7846 | 28.2821 | 16.7632 | 20 | 1.9162 | -0.087 | 0.8844 | 1.2298 | -0.4517 | 3.2907 | 0.0978 | -0.6345 | -0.1659 | 0.3069 | -0.0178 | 0.0667 | 0.235 | -0.4408 | -0.08 | -0.0979 | -0.0845 | -0.031 | 0.0094 | 0.0506 | -0.1943 | 32.051 | 29.7663 | 32.9791 | 21 | 4.436 | 1.2827 | 1.3864 | 1.3044 | -0.058 | 1.3822 | 0.1453 | -0.2868 | -0.0675 | 0.4842 | 0.1313 | -0.4355 | 0.455 | 0.1734 | -0.2766 | -0.0839 | 0.0736 | -0.1949 | 0.0126 | -0.1555 | -0.1202 | 50.9398 | 38.8258 | 37.1225 | 22 | 2.3916 | 0.9155 | -1.6227 | 4.2455 | 2.9982 | 3.1827 | 0.0355 | -0.0285 | 0.5133 | 0.0095 | -0.1568 | 0.2447 | 0.004 | 0.0224 | 0.1213 | -0.0507 | -0.0479 | -0.1789 | 0.1803 | -0.1672 | -0.0855 | 42.9403 | 49.7204 | 38.9494 | 23 | 0.8757 | 2.0251 | 1.1158 | 6.7392 | 2.9321 | 0.7195 | -0.0109 | 0.0553 | 0.1701 | 0.0231 | -0.0132 | -0.0376 | -0.1184 | -0.0577 | 0.0241 | -0.1177 | 0.0444 | -0.1689 | 0.257 | -0.0695 | -0.1431 | 53.9943 | 52.6421 | 37.2364 | 24 | 0 | 1.5875 | 3.39 | 0.0021 | 2.9284 | 4.6849 | -0.0083 | 0.0325 | -0.0082 | 0.0475 | 0.0823 | -0.2674 | -0.0434 | -0.0586 | -0.074 | -0.1269 | 0.0105 | -0.1371 | 0.2565 | -0.1318 | -0.0825 | 56.221 | 48.1025 | 34.3272 |
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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 | {A|-12 - 38} | 2 | X-RAY DIFFRACTION | 2 | {A|39 - 96} | 3 | X-RAY DIFFRACTION | 3 | {A|97 - 146} | 4 | X-RAY DIFFRACTION | 4 | {A|147 - 199} | 5 | X-RAY DIFFRACTION | 5 | {A|200 - 243} | 6 | X-RAY DIFFRACTION | 6 | {A|244 - 335} | 7 | X-RAY DIFFRACTION | 7 | {A|336 - 361} | 8 | X-RAY DIFFRACTION | 8 | {A|362 - 388} | 9 | X-RAY DIFFRACTION | 9 | {A|389 - 399} | 10 | X-RAY DIFFRACTION | 10 | {A|400 - 448} | 11 | X-RAY DIFFRACTION | 11 | {A|449 - 484} | 12 | X-RAY DIFFRACTION | 12 | {A|485 - 510} | 13 | X-RAY DIFFRACTION | 13 | {B|-13 - 47} | 14 | X-RAY DIFFRACTION | 14 | {B|48 - 83} | 15 | X-RAY DIFFRACTION | 15 | {B|84 - 100} | 16 | X-RAY DIFFRACTION | 16 | {B|101 - 140} | 17 | X-RAY DIFFRACTION | 17 | {B|141 - 159} | 18 | X-RAY DIFFRACTION | 18 | {B|160 - 199} | 19 | X-RAY DIFFRACTION | 19 | {B|200 - 232} | 20 | X-RAY DIFFRACTION | 20 | {B|233 - 372} | 21 | X-RAY DIFFRACTION | 21 | {B|373 - 425} | 22 | X-RAY DIFFRACTION | 22 | {B|426 - 460} | 23 | X-RAY DIFFRACTION | 23 | {B|461 - 486} | 24 | X-RAY DIFFRACTION | 24 | {B|487 - 510} |
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