ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0258精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | 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: 3IXF 解像度: 1.563→37.3 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.995 / SU ML: 0.058 / 交差検証法: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.097 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2161 | 1951 | 5.24 % |
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Rwork | 0.1836 | - | - |
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all | 0.185 | - | - |
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obs | - | 37232 | 94.483 % |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å |
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原子変位パラメータ | Biso mean: 18.272 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.891 Å2 | 0 Å2 | -0 Å2 |
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2- | - | -0.444 Å2 | 0 Å2 |
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3- | - | - | -0.447 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.563→37.3 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2159 | 0 | 124 | 169 | 2452 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.012 | 0.013 | 2627 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.018 | 2330 | X-RAY DIFFRACTION | r_angle_refined_deg2.001 | 1.645 | 3607 | X-RAY DIFFRACTION | r_angle_other_deg1.636 | 1.576 | 5473 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.962 | 5 | 343 | X-RAY DIFFRACTION | r_dihedral_angle_other_1_deg0.579 | 10 | 1 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.34 | 23.333 | 135 | X-RAY DIFFRACTION | r_dihedral_angle_other_2_deg11.652 | 10 | 15 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.391 | 15 | 474 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg26.497 | 15 | 16 | X-RAY DIFFRACTION | r_chiral_restr0.101 | 0.2 | 316 | X-RAY DIFFRACTION | r_gen_planes_refined0.011 | 0.02 | 3101 | X-RAY DIFFRACTION | r_gen_planes_other0.003 | 0.02 | 566 | X-RAY DIFFRACTION | r_nbd_refined0.252 | 0.2 | 646 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.184 | 0.2 | 2142 | X-RAY DIFFRACTION | r_nbtor_refined0.192 | 0.2 | 1264 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.085 | 0.2 | 1051 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.158 | 0.2 | 135 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.058 | 0.2 | 1 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.297 | 0.2 | 31 | X-RAY DIFFRACTION | r_nbd_other0.291 | 0.2 | 73 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.135 | 0.2 | 27 | X-RAY DIFFRACTION | r_mcbond_it0.872 | 1.347 | 1242 | X-RAY DIFFRACTION | r_mcbond_other0.871 | 1.347 | 1241 | X-RAY DIFFRACTION | r_mcangle_it1.311 | 2.025 | 1588 | X-RAY DIFFRACTION | r_mcangle_other1.311 | 2.026 | 1589 | X-RAY DIFFRACTION | r_scbond_it1.584 | 1.573 | 1385 | X-RAY DIFFRACTION | r_scbond_other1.561 | 1.569 | 1378 | X-RAY DIFFRACTION | r_scangle_it2.4 | 2.297 | 2002 | X-RAY DIFFRACTION | r_scangle_other2.371 | 2.289 | 1991 | X-RAY DIFFRACTION | r_lrange_it3.671 | 16.574 | 3207 | X-RAY DIFFRACTION | r_lrange_other3.638 | 16.441 | 3186 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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1.563-1.603 | 0.333 | 146 | 0.241 | 2132 | X-RAY DIFFRACTION | 78.9875 | 1.603-1.647 | 0.275 | 117 | 0.214 | 2426 | X-RAY DIFFRACTION | 90.9514 | 1.647-1.695 | 0.258 | 126 | 0.209 | 2469 | X-RAY DIFFRACTION | 95.2993 | 1.695-1.747 | 0.227 | 119 | 0.194 | 2479 | X-RAY DIFFRACTION | 98.0747 | 1.747-1.804 | 0.216 | 118 | 0.168 | 2379 | X-RAY DIFFRACTION | 97.9984 | 1.804-1.868 | 0.211 | 134 | 0.169 | 2309 | X-RAY DIFFRACTION | 98.0337 | 1.868-1.938 | 0.21 | 148 | 0.175 | 2192 | X-RAY DIFFRACTION | 97.622 | 1.938-2.017 | 0.206 | 129 | 0.165 | 2119 | X-RAY DIFFRACTION | 97.3582 | 2.017-2.106 | 0.233 | 100 | 0.17 | 2064 | X-RAY DIFFRACTION | 96.91 | 2.106-2.209 | 0.194 | 95 | 0.167 | 1985 | X-RAY DIFFRACTION | 96.8343 | 2.209-2.328 | 0.226 | 100 | 0.174 | 1844 | X-RAY DIFFRACTION | 96.4764 | 2.328-2.469 | 0.158 | 100 | 0.161 | 1748 | X-RAY DIFFRACTION | 95.0617 | 2.469-2.639 | 0.199 | 96 | 0.167 | 1632 | X-RAY DIFFRACTION | 95.8935 | 2.639-2.85 | 0.225 | 72 | 0.182 | 1545 | X-RAY DIFFRACTION | 95.2297 | 2.85-3.121 | 0.239 | 80 | 0.193 | 1416 | X-RAY DIFFRACTION | 94.8036 | 3.121-3.487 | 0.227 | 75 | 0.206 | 1266 | X-RAY DIFFRACTION | 94.0393 | 3.487-4.023 | 0.204 | 77 | 0.185 | 1125 | X-RAY DIFFRACTION | 93.9797 | 4.023-4.919 | 0.167 | 53 | 0.167 | 957 | X-RAY DIFFRACTION | 92.3218 | 4.919-6.92 | 0.242 | 39 | 0.223 | 766 | X-RAY DIFFRACTION | 92.4225 | 6.92-37.3 | 0.272 | 27 | 0.212 | 428 | X-RAY DIFFRACTION | 87.5 |
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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 | 0.3019 | -0.0255 | -0.0347 | 0.3449 | -0.119 | 0.1878 | -0.0285 | -0.0704 | -0.002 | -0.0027 | 0.0048 | -0.0506 | 0.0008 | 0.0046 | 0.0237 | 0.0376 | -0.0083 | 0.0032 | 0.0457 | -0.0011 | 0.0333 | -14.7682 | 7.0724 | -15.3554 | 2 | 1.6725 | 1.0841 | 0.3163 | 3.0804 | 2.0747 | 1.5406 | -0.0888 | 0.089 | -0.087 | 0.0001 | 0.1029 | -0.0116 | 0.0216 | 0.0238 | -0.014 | 0.0095 | 0.0139 | 0.024 | 0.1096 | 0.0713 | 0.1043 | -31.1903 | -1.473 | -12.4194 | 3 | 1.7491 | -1.1389 | 2.951 | 9.2222 | -4.8597 | 5.9972 | 0.1504 | 0.1167 | -0.1527 | -0.0959 | 0.1092 | 0.0886 | 0.2562 | 0.1297 | -0.2596 | 0.0484 | -0.0181 | -0.001 | 0.0507 | -0.0078 | 0.0457 | -26.861 | -9.8607 | -15.9902 | 4 | 0.9241 | 0.1828 | -0.5149 | 0.3911 | -0.1928 | 0.9591 | -0.0763 | 0.0065 | -0.0617 | -0.0122 | -0.0079 | -0.0266 | 0.0783 | 0.0264 | 0.0842 | 0.0532 | 0.0088 | 0.0057 | 0.0273 | -0.0029 | 0.0264 | -17.4249 | -6.1293 | -11.8206 | 5 | 0.3887 | -0.3366 | -0.051 | 0.5059 | -0.3805 | 0.8625 | 0.0562 | 0.0301 | 0.0011 | -0.0666 | -0.0555 | -0.0023 | 0.0313 | 0.0286 | -0.0008 | 0.0409 | 0.0049 | -0.0022 | 0.0519 | -0.0051 | 0.0334 | -17.1035 | 8.2989 | -29.734 | 6 | 1.8409 | -1.4871 | -0.6168 | 2.9864 | -0.3965 | 0.6551 | 0.059 | 0.03 | -0.106 | -0.2553 | -0.0637 | 0.1709 | 0.0934 | 0.0146 | 0.0047 | 0.1265 | -0.0241 | -0.0598 | 0.0289 | -0.0047 | 0.0458 | -23.4439 | -5.1814 | -30.668 | 7 | 1.7196 | -1.5659 | -1.0034 | 3.7885 | 2.3604 | 1.4741 | 0.009 | 0.009 | -0.0532 | -0.045 | 0.0083 | -0.0091 | -0.0173 | -0.007 | -0.0174 | 0.0446 | -0.0528 | -0.0391 | 0.0752 | 0.0461 | 0.0493 | -30.3925 | 2.0498 | -22.9476 | 8 | 1.1711 | 0.8123 | 0.0192 | 2.3787 | 1.926 | 2.0311 | -0.0128 | -0.0395 | 0.1585 | -0.0061 | 0.0444 | 0.0871 | 0.0058 | 0.0398 | -0.0316 | 0.032 | 0.0031 | 0.0033 | 0.0861 | 0.0134 | 0.0402 | -23.0281 | 11.2459 | -13.6794 | 9 | 1.2234 | 0.2821 | 1.0812 | 1.0662 | 0.9192 | 1.5586 | 0.0718 | -0.0847 | 0.0737 | 0.0003 | -0.0325 | 0.0263 | 0.0574 | -0.1006 | -0.0393 | 0.0216 | -0.0097 | 0.0022 | 0.0604 | 0.0004 | 0.0827 | -21.663 | 15.3899 | -20.2398 | 10 | 0.65 | 0.2264 | 1.0822 | 0.3922 | 1.274 | 4.3723 | 0.0902 | -0.0612 | -0.0377 | -0.0074 | -0.081 | 0.0073 | 0.0498 | -0.2792 | -0.0092 | 0.0718 | -0.0201 | -0.034 | 0.0762 | 0.0019 | 0.0171 | -30.1667 | 4.359 | -32.227 | 11 | 0.1878 | -0.0067 | 0.1449 | 0.0887 | -0.137 | 0.4728 | 0.003 | 0.0038 | -0.0636 | 0.0003 | 0.025 | -0.0146 | -0.0274 | -0.0443 | -0.028 | 0.0326 | 0.0029 | -0.0092 | 0.0409 | 0.0096 | 0.0476 | 2.5499 | -1.8949 | -23.8556 | 12 | 0.2773 | -1.1213 | -0.35 | 4.9964 | 0.9161 | 0.9948 | -0.0255 | 0.0127 | 0.0096 | 0.0996 | -0.148 | -0.1871 | 0.0413 | 0.0627 | 0.1735 | 0.0291 | 0.0024 | -0.015 | 0.073 | -0.0126 | 0.0953 | 13.0294 | -3.0864 | -9.5569 | 13 | 2.0837 | -2.8646 | 1.1681 | 4.5016 | -0.4889 | 3.0161 | 0.0443 | -0.1737 | -0.2742 | -0.0199 | 0.2036 | 0.3075 | 0.0697 | -0.0699 | -0.2479 | 0.0175 | -0.032 | -0.0116 | 0.081 | 0.0527 | 0.0825 | 3.2295 | -10.9524 | -10.161 | 14 | 1.4492 | -0.0495 | -0.4836 | 1.4005 | -0.6634 | 1.7301 | -0.0841 | -0.03 | -0.0223 | 0.0808 | 0.0361 | -0.0315 | 0.0251 | -0.0676 | 0.048 | 0.0292 | 0.0097 | 0.0022 | 0.046 | 0.0158 | 0.0355 | 0.4359 | 0.7882 | -13.311 | 15 | 0.5839 | 0.6202 | -0.4053 | 1.0846 | -0.908 | 0.8184 | 0.0281 | -0.0209 | 0.0489 | 0.0415 | 0.0113 | 0.061 | -0.04 | -0.0175 | -0.0395 | 0.0475 | -0.0008 | 0.0004 | 0.041 | 0.0091 | 0.0429 | 2.5 | 12.2381 | -27.2515 | 16 | 0.1374 | 0.5819 | 0.6082 | 2.4998 | 2.559 | 2.6985 | 0.0297 | -0.0143 | 0.0051 | 0.1502 | -0.0858 | -0.0325 | 0.0703 | -0.05 | 0.0562 | 0.124 | -0.0925 | -0.0658 | 0.0849 | 0.0169 | 0.1031 | 8.1431 | 15.7834 | -18.3951 | 17 | 6.1467 | -2.1679 | -3.4834 | 0.8024 | 1.5869 | 5.3782 | 0.1574 | -0.3699 | 0.0894 | -0.053 | 0.1186 | -0.0543 | -0.0447 | 0.0901 | -0.276 | 0.0764 | -0.054 | -0.0331 | 0.0536 | 0.02 | 0.0332 | 13.1739 | 9.9764 | -12.9897 | 18 | 2.4805 | 0.5265 | 1.5094 | 1.5618 | 0.9708 | 1.2117 | 0.072 | 0.1184 | 0.0032 | 0.0872 | -0.0648 | -0.0505 | 0.0701 | 0.0326 | -0.0071 | 0.0382 | -0.0035 | -0.019 | 0.0353 | 0.0229 | 0.0667 | 10.4683 | -1.3486 | -26.8728 | 19 | 2.6984 | 2.477 | 1.3502 | 2.8615 | 1.3782 | 1.0149 | 0.005 | 0.1035 | -0.0429 | 0.0316 | 0.038 | -0.0956 | 0.0168 | 0.0517 | -0.0429 | 0.0351 | 0.0011 | -0.0089 | 0.0282 | 0.001 | 0.0427 | 7.2981 | 3.525 | -32.926 | 20 | 0.4497 | -0.501 | 0.0158 | 4.8974 | 2.1369 | 1.0751 | 0.0823 | -0.0081 | -0.1148 | -0.0201 | 0.1012 | -0.2573 | 0.0156 | 0.052 | -0.1834 | 0.1005 | -0.0483 | -0.0493 | 0.0416 | -0.0001 | 0.0748 | 15.7611 | 14.7125 | -22.386 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | ALLA1 - 26 | 2 | X-RAY DIFFRACTION | 2 | ALLA27 - 33 | 3 | X-RAY DIFFRACTION | 3 | ALLA34 - 37 | 4 | X-RAY DIFFRACTION | 4 | ALLA38 - 60 | 5 | X-RAY DIFFRACTION | 5 | ALLA61 - 83 | 6 | X-RAY DIFFRACTION | 6 | ALLA84 - 90 | 7 | X-RAY DIFFRACTION | 7 | ALLA91 - 99 | 8 | X-RAY DIFFRACTION | 8 | ALLA100 - 111 | 9 | X-RAY DIFFRACTION | 9 | ALLA112 - 128 | 10 | X-RAY DIFFRACTION | 10 | ALLA129 - 137 | 11 | X-RAY DIFFRACTION | 11 | ALLB1 - 30 | 12 | X-RAY DIFFRACTION | 12 | ALLB31 - 39 | 13 | X-RAY DIFFRACTION | 13 | ALLB40 - 50 | 14 | X-RAY DIFFRACTION | 14 | ALLB51 - 60 | 15 | X-RAY DIFFRACTION | 15 | ALLB61 - 77 | 16 | X-RAY DIFFRACTION | 16 | ALLB78 - 86 | 17 | X-RAY DIFFRACTION | 17 | ALLB87 - 94 | 18 | X-RAY DIFFRACTION | 18 | ALLB95 - 111 | 19 | X-RAY DIFFRACTION | 19 | ALLB112 - 128 | 20 | X-RAY DIFFRACTION | 20 | ALLB129 - 137 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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