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 | | REFMAC | 5.2.0019精密化 | | PDB_EXTRACT | 3.006 | データ抽出 | | SBC-Collect | | データ収集 | | SHELXD | | 位相決定 | | MLPHARE | | 位相決定 | | 直接法 | | 位相決定 | | SOLVE | | 位相決定 | | RESOLVE | | 位相決定 | | HKL-3000 | | 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: 2.1→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.13 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.122 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.193 | 1225 | 5.1 % | RANDOM |
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Rwork | 0.172 | - | - | - |
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all | 0.173 | 23940 | - | - |
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obs | 0.173 | 23940 | 95.39 % | - |
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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 / 溶媒モデル: MASK |
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原子変位パラメータ | Biso max: 69.42 Å2 / Biso mean: 49.399 Å2 / Biso min: 23.37 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.87 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -1.87 Å2 | 0 Å2 |
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3- | - | - | 3.75 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.1→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1643 | 0 | 49 | 154 | 1846 |
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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_d0.018 | 0.022 | 1826 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 1244 | X-RAY DIFFRACTION | r_angle_refined_deg1.705 | 1.997 | 2502 | X-RAY DIFFRACTION | r_angle_other_deg1.058 | 3 | 3063 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.278 | 5 | 242 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.226 | 24.405 | 84 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg14.907 | 15 | 330 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg17.189 | 15 | 15 | X-RAY DIFFRACTION | r_chiral_restr0.098 | 0.2 | 287 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 2036 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 349 | X-RAY DIFFRACTION | r_nbd_refined0.21 | 0.2 | 321 | X-RAY DIFFRACTION | r_nbd_other0.209 | 0.2 | 1301 | X-RAY DIFFRACTION | r_nbtor_refined0.17 | 0.2 | 831 | X-RAY DIFFRACTION | r_nbtor_other0.087 | 0.2 | 952 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.191 | 0.2 | 113 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.127 | 0.2 | 7 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.272 | 0.2 | 24 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.217 | 0.2 | 6 | X-RAY DIFFRACTION | r_mcbond_it0.767 | 1.5 | 1382 | X-RAY DIFFRACTION | r_mcbond_other0.22 | 1.5 | 451 | X-RAY DIFFRACTION | r_mcangle_it0.995 | 2 | 1813 | X-RAY DIFFRACTION | r_scbond_it2.027 | 3 | 786 | X-RAY DIFFRACTION | r_scangle_it2.643 | 4.5 | 673 | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.095→2.149 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.339 | 67 | - |
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Rwork | 0.268 | 1282 | - |
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all | - | 1349 | - |
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obs | - | 1349 | 73.92 % |
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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 | 12.882 | 0.8622 | 6.3758 | 27.6135 | 10.0455 | 9.7356 | 0.2173 | 0.7586 | -1.1854 | -0.5668 | -0.2329 | 0.6417 | 0.159 | -0.2159 | 0.0157 | -0.2014 | 0.056 | 0.0318 | 0.0115 | -0.0034 | -0.0449 | 38.2748 | 14.1714 | 12.422 | 2 | 19.0837 | -10.4936 | 2.8085 | 8.8843 | -7.8559 | 14.1683 | -0.058 | 0.4534 | 0.4294 | 0.1698 | -0.0367 | -0.3453 | -1.1662 | 0.877 | 0.0946 | -0.0236 | -0.0747 | 0.0208 | -0.1178 | 0.0432 | -0.0172 | 48.8794 | 22.801 | 18.8619 | 3 | 0.7953 | -1.5282 | -0.3277 | 4.6651 | -3.6534 | 10.7469 | -0.1245 | 0.2093 | -0.0404 | 0.2736 | 0.1404 | -0.3746 | -0.3384 | 0.6265 | -0.0158 | -0.2014 | -0.0025 | 0.0184 | -0.1713 | -0.0237 | -0.053 | 49.006 | 14.0512 | 17.2449 | 4 | 6.928 | -7.4182 | 1.2204 | 16.245 | 0.1243 | 2.3882 | 0.0472 | 0.5259 | -0.4921 | -0.2963 | -0.15 | -0.2715 | 0.41 | -0.1382 | 0.1028 | -0.1363 | -0.0021 | 0.0416 | -0.1366 | -0.0456 | -0.0184 | 44.9097 | 10.1712 | 11.9529 | 5 | 34.3578 | -8.9044 | -2.4918 | 8.0876 | 4.2425 | 17.8405 | 0.6881 | 0.839 | 2.68 | -0.2258 | 0.2927 | -0.3626 | -1.2431 | 0.3729 | -0.9809 | -0.0201 | 0.0571 | 0.1218 | -0.0496 | 0.0878 | 0.1717 | 42.7854 | 29.3596 | 11.207 | 6 | 13.9898 | -6.5158 | -5.6327 | 4.6489 | 1.2239 | 3.4815 | 0.3606 | 0.2023 | 0.6301 | -0.3131 | -0.0791 | -0.3975 | -0.4881 | -0.1418 | -0.2815 | -0.12 | 0.0102 | 0.0077 | -0.0854 | 0.0558 | -0.1106 | 46.149 | 23.7353 | 9.4616 | 7 | 5.1207 | -2.4704 | 1.3359 | 40.9289 | 19.8403 | 11.4424 | 0.0049 | 0.3787 | 0.1976 | -0.7127 | 0.2509 | 1.3919 | -0.5725 | -0.3667 | -0.2558 | -0.0712 | 0.0747 | 0.0133 | 0.0653 | 0.1268 | -0.003 | 31.9063 | 26.0961 | 11.403 | 8 | 6.8884 | -3.0142 | -1.3981 | 4.3831 | 3.0709 | 6.7239 | 0.0251 | 0.1114 | 0.1445 | -0.017 | 0.1807 | -0.0719 | -0.3051 | -0.022 | -0.2058 | -0.2403 | 0.0289 | 0.0133 | -0.1524 | 0.0842 | -0.0711 | 37.5174 | 19.8768 | 18.2802 | 9 | 52.5211 | 1.6429 | 1.5162 | 39.3915 | 9.0196 | 2.09 | 0.4541 | 1.7705 | 1.2766 | -0.2089 | 1.5245 | -4.0739 | 0.3298 | 1.7722 | -1.9785 | 0.1249 | 0.006 | 0.0055 | 0.2782 | -0.1852 | 0.5558 | 44.2673 | 35.6764 | 27.6672 | 10 | 4.0221 | -2.2802 | 0.4564 | 8.5217 | -0.3368 | 4.9746 | -0.0763 | -0.0667 | 0.421 | 0.0566 | 0.1685 | -0.4894 | -0.3276 | 0.2513 | -0.0922 | -0.1816 | 0.0741 | 0.0402 | -0.1394 | 0.0435 | 0.0247 | 34.304 | 30.8774 | 25.4271 | 11 | 3.0458 | 0.1903 | -0.6595 | 8.3259 | -0.064 | 5.3184 | 0.115 | 0.5663 | 0.0515 | -0.4386 | -0.157 | 0.8235 | -0.2621 | -0.7749 | 0.042 | -0.1852 | 0.0577 | -0.0142 | -0.0115 | 0.0234 | 0.0291 | 28.2017 | 18.23 | 17.7643 | 12 | 1.758 | -0.612 | -1.1622 | 3.3058 | 5.8129 | 10.226 | -0.2488 | 0.0641 | 0.1578 | -0.0802 | 0.1384 | 0.0991 | -0.8053 | -0.2964 | 0.1104 | -0.1512 | 0.0299 | 0.0148 | -0.188 | -0.0016 | 0.0409 | 38.9396 | 18.6713 | 31.735 | 13 | 5.3832 | 0.9198 | 5.0245 | 17.7268 | -6.9833 | 14.147 | -0.2677 | -0.6029 | 0.4211 | 0.5948 | -0.0585 | -1.2454 | -0.115 | 1.1278 | 0.3262 | -0.0943 | 0.1007 | -0.0658 | 0.0004 | -0.0825 | 0.1868 | 40.2123 | 28.8265 | 41.7571 | 14 | 13.0307 | 0.6579 | 6.6491 | 2.4541 | 1.9383 | 4.4537 | -0.0225 | -0.4633 | -0.0612 | 0.175 | 0.0781 | -0.0772 | 0.095 | -0.0269 | -0.0556 | -0.1732 | 0.0622 | -0.0023 | -0.1783 | 0.0075 | -0.0359 | 35.1045 | 24.441 | 33.7703 | 15 | 5.5133 | -0.5634 | 0.5304 | 2.5566 | 0.3128 | 2.34 | -0.1623 | -0.1504 | 0.0413 | 0.117 | 0.1338 | 0.098 | -0.1351 | -0.1524 | 0.0284 | -0.1892 | 0.0367 | 0.0145 | -0.2266 | 0.036 | -0.0983 | 35.8394 | 16.68 | 29.3595 | 16 | 8.8033 | -1.7242 | -5.3269 | 5.0064 | 0.2502 | 7.9334 | -0.1345 | -0.9216 | -0.0505 | 0.5355 | 0.211 | -0.2728 | -0.055 | 0.7029 | -0.0764 | -0.1345 | 0.0608 | -0.0991 | -0.1105 | 0.0277 | -0.0316 | 49.1479 | 11.4468 | 36.2938 | 17 | 9.0305 | 3.0373 | 3.49 | 4.1757 | 1.3987 | 4.2284 | -0.0984 | 0.123 | -0.1581 | 0.1927 | 0.0902 | -0.2062 | 0.024 | 0.1497 | 0.0081 | -0.206 | 0.03 | -0.0032 | -0.2235 | 0.0244 | -0.0703 | 46.9871 | 11.0053 | 26.1073 | 18 | 2.3532 | -1.5715 | 0.7321 | 2.5173 | 1.1084 | 1.9658 | -0.06 | -0.3439 | -0.0403 | 0.3813 | -0.0217 | 0.1439 | 0.1791 | -0.1507 | 0.0818 | -0.1587 | 0.0072 | -0.0005 | -0.1866 | 0.061 | -0.0906 | 40.0574 | 8.8184 | 31.6632 | 19 | 17.8011 | 2.8185 | 4.001 | 9.4664 | -4.0356 | 3.3161 | 0.0222 | -0.8154 | -0.2361 | 0.3034 | 0.0603 | -0.2581 | 0.3073 | 0.0771 | -0.0825 | -0.1158 | 0.056 | 0.008 | -0.1731 | 0.0092 | -0.054 | 46.6296 | 1.4774 | 30.6689 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | X-RAY DIFFRACTION | 1 | AA0 - 6 | 21 - 27 | 2 | X-RAY DIFFRACTION | 2 | AA7 - 14 | 28 - 35 | 3 | X-RAY DIFFRACTION | 3 | AA15 - 20 | 36 - 41 | 4 | X-RAY DIFFRACTION | 4 | AA21 - 29 | 42 - 50 | 5 | X-RAY DIFFRACTION | 5 | AA30 - 34 | 51 - 55 | 6 | X-RAY DIFFRACTION | 6 | AA35 - 54 | 56 - 75 | 7 | X-RAY DIFFRACTION | 7 | AA55 - 62 | 76 - 83 | 8 | X-RAY DIFFRACTION | 8 | AA63 - 74 | 84 - 95 | 9 | X-RAY DIFFRACTION | 9 | AA75 - 80 | 96 - 101 | 10 | X-RAY DIFFRACTION | 10 | AA81 - 91 | 102 - 112 | 11 | X-RAY DIFFRACTION | 11 | AA92 - 105 | 113 - 126 | 12 | X-RAY DIFFRACTION | 12 | AA106 - 114 | 127 - 135 | 13 | X-RAY DIFFRACTION | 13 | AA115 - 125 | 136 - 146 | 14 | X-RAY DIFFRACTION | 14 | AA126 - 135 | 147 - 156 | 15 | X-RAY DIFFRACTION | 15 | AA136 - 154 | 157 - 175 | 16 | X-RAY DIFFRACTION | 16 | AA155 - 171 | 176 - 192 | 17 | X-RAY DIFFRACTION | 17 | AA172 - 190 | 193 - 211 | 18 | X-RAY DIFFRACTION | 18 | AA191 - 202 | 212 - 223 | 19 | X-RAY DIFFRACTION | 19 | AA203 - 213 | 224 - 234 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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