ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0267精密化 | HKL-2000 | | データ削減 | HKL-3000 | | データスケーリング | MOLREP | | 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: 7STT 解像度: 2.23→39.217 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.177 / SU ML: 0.164 / 交差検証法: FREE R-VALUE / ESU R: 0.302 / ESU R Free: 0.215 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2252 | 1205 | 5.235 % |
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Rwork | 0.1738 | 21815 | - |
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all | 0.176 | - | - |
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obs | - | 23020 | 99.19 % |
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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: BABINET MODEL PLUS MASK |
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原子変位パラメータ | Biso mean: 33.47 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.13 Å2 | 0.565 Å2 | 0 Å2 |
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2- | - | 1.13 Å2 | -0 Å2 |
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3- | - | - | -3.664 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.23→39.217 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3495 | 0 | 9 | 316 | 3820 |
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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_d0.007 | 0.013 | 3586 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.015 | 3292 | X-RAY DIFFRACTION | r_angle_refined_deg1.382 | 1.65 | 4862 | X-RAY DIFFRACTION | r_angle_other_deg1.331 | 1.583 | 7583 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.433 | 5 | 444 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg31.014 | 22.335 | 197 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg12.44 | 15 | 576 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg11.544 | 15 | 23 | X-RAY DIFFRACTION | r_chiral_restr0.064 | 0.2 | 448 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 4142 | X-RAY DIFFRACTION | r_gen_planes_other0.002 | 0.02 | 868 | X-RAY DIFFRACTION | r_nbd_refined0.209 | 0.2 | 811 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.192 | 0.2 | 3191 | X-RAY DIFFRACTION | r_nbtor_refined0.164 | 0.2 | 1758 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.08 | 0.2 | 1449 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.135 | 0.2 | 307 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.067 | 0.2 | 1 | X-RAY DIFFRACTION | r_metal_ion_refined0.139 | 0.2 | 14 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.248 | 0.2 | 23 | X-RAY DIFFRACTION | r_nbd_other0.196 | 0.2 | 85 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.1 | 0.2 | 9 | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined0.236 | 0.2 | 1 | X-RAY DIFFRACTION | r_mcbond_it1.042 | 2.486 | 1779 | X-RAY DIFFRACTION | r_mcbond_other1.039 | 2.485 | 1778 | X-RAY DIFFRACTION | r_mcangle_it1.831 | 3.726 | 2222 | X-RAY DIFFRACTION | r_mcangle_other1.831 | 3.728 | 2223 | X-RAY DIFFRACTION | r_scbond_it1.105 | 2.58 | 1807 | X-RAY DIFFRACTION | r_scbond_other1.105 | 2.581 | 1808 | X-RAY DIFFRACTION | r_scangle_it1.901 | 3.811 | 2640 | X-RAY DIFFRACTION | r_scangle_other1.901 | 3.811 | 2640 | X-RAY DIFFRACTION | r_lrange_it6.29 | 30.602 | 4299 | X-RAY DIFFRACTION | r_lrange_other6.134 | 30.058 | 4245 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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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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2.23-2.288 | 0.319 | 102 | 0.282 | 1553 | X-RAY DIFFRACTION | 99.3397 | 2.288-2.35 | 0.308 | 78 | 0.218 | 1560 | X-RAY DIFFRACTION | 99.7564 | 2.35-2.418 | 0.226 | 81 | 0.195 | 1523 | X-RAY DIFFRACTION | 99.442 | 2.418-2.492 | 0.251 | 101 | 0.172 | 1440 | X-RAY DIFFRACTION | 99.8704 | 2.492-2.574 | 0.22 | 66 | 0.175 | 1424 | X-RAY DIFFRACTION | 98.6755 | 2.574-2.664 | 0.186 | 74 | 0.164 | 1375 | X-RAY DIFFRACTION | 99.8622 | 2.664-2.764 | 0.204 | 77 | 0.171 | 1348 | X-RAY DIFFRACTION | 99.7899 | 2.764-2.876 | 0.238 | 77 | 0.168 | 1269 | X-RAY DIFFRACTION | 100 | 2.876-3.003 | 0.24 | 79 | 0.171 | 1234 | X-RAY DIFFRACTION | 99.9239 | 3.003-3.149 | 0.249 | 49 | 0.181 | 1200 | X-RAY DIFFRACTION | 100 | 3.149-3.318 | 0.242 | 64 | 0.19 | 1145 | X-RAY DIFFRACTION | 100 | 3.318-3.518 | 0.226 | 61 | 0.189 | 1042 | X-RAY DIFFRACTION | 98.6583 | 3.518-3.759 | 0.25 | 52 | 0.173 | 986 | X-RAY DIFFRACTION | 96.9188 | 3.759-4.057 | 0.209 | 38 | 0.151 | 940 | X-RAY DIFFRACTION | 97.1202 | 4.057-4.439 | 0.197 | 38 | 0.14 | 860 | X-RAY DIFFRACTION | 97.1861 | 4.439-4.956 | 0.233 | 40 | 0.145 | 800 | X-RAY DIFFRACTION | 98.476 | 4.956-5.708 | 0.143 | 30 | 0.167 | 719 | X-RAY DIFFRACTION | 99.8667 | 5.708-6.955 | 0.239 | 35 | 0.164 | 616 | X-RAY DIFFRACTION | 100 | 6.955-9.691 | 0.193 | 47 | 0.153 | 461 | X-RAY DIFFRACTION | 97.6923 | 9.691-39.217 | 0.175 | 15 | 0.193 | 312 | X-RAY DIFFRACTION | 99.6951 |
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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 | 0.5928 | 0.0821 | -0.1289 | 0.4738 | 0.0821 | 0.5364 | 0.0274 | 0.0725 | -0.1076 | 0.0271 | -0.0351 | -0.0193 | 0.0679 | -0.0429 | 0.0078 | 0.0948 | -0.0163 | -0.0184 | 0.1043 | -0.0253 | 0.0241 | -27.0224 | 18.6896 | 19.3851 | 2 | 3.1167 | 0.6602 | 1.1357 | 0.9114 | 0.023 | 1.0701 | -0.0211 | 0.0511 | -0.3739 | 0.0115 | -0.0762 | -0.3301 | 0.0474 | 0.0126 | 0.0973 | 0.1446 | 0.0199 | -0.0309 | 0.1274 | -0.0074 | 0.2025 | -6.4504 | 14.1716 | 16.48 | 3 | 1.4097 | 0.7196 | 0.7083 | 0.7743 | 0.3791 | 0.9707 | -0.0177 | 0.1395 | 0.0267 | -0.0748 | -0.0224 | -0.0175 | 0.0239 | -0.0718 | 0.0401 | 0.0925 | -0.0053 | 0.0001 | 0.1647 | -0.0062 | 0.0058 | -24.7936 | 27.352 | 9.676 | 4 | 1.1359 | -0.0284 | -0.0288 | 0.765 | 0.0181 | 0.6549 | 0.0921 | 0.047 | 0.1336 | -0.0052 | -0.0473 | -0.0804 | -0.097 | -0.0151 | -0.0448 | 0.0878 | 0.0047 | 0.0058 | 0.0949 | 0.0196 | 0.0285 | -19.7573 | 43.9494 | 18.0476 |
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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 - 209 | 2 | X-RAY DIFFRACTION | 2 | ALLA210 - 260 | 3 | X-RAY DIFFRACTION | 3 | ALLA261 - 344 | 4 | X-RAY DIFFRACTION | 4 | ALLA345 - 445 | | | | | | | | |
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