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 | | 精密化 | | PDB_EXTRACT | 3.006 | データ抽出 | | SBC-Collect | | データ収集 | | HKL-3000 | | データ削減 | | 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: 1.94→33 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.881 / SU B: 5.352 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.121 / 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 | 0.202 | 626 | 4.9 % | RANDOM |
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Rwork | 0.169 | - | - | - |
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all | 0.171 | 12850 | - | - |
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obs | 0.171 | 12850 | 99.95 % | - |
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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: 74.78 Å2 / Biso mean: 42.192 Å2 / Biso min: 25.29 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.37 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.37 Å2 | 0 Å2 |
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3- | - | - | 0.74 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.94→33 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1003 | 0 | 5 | 89 | 1097 |
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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_d0.019 | 0.022 | 1080 | X-RAY DIFFRACTION | r_angle_refined_deg1.631 | 1.967 | 1469 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.372 | 5 | 132 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg29.592 | 24.182 | 55 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg17.244 | 15 | 201 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg21.669 | 15 | 6 | X-RAY DIFFRACTION | r_chiral_restr0.126 | 0.2 | 156 | X-RAY DIFFRACTION | r_gen_planes_refined0.008 | 0.02 | 821 | X-RAY DIFFRACTION | r_nbd_refined0.226 | 0.2 | 466 | X-RAY DIFFRACTION | r_nbtor_refined0.312 | 0.2 | 744 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.145 | 0.2 | 73 | X-RAY DIFFRACTION | r_metal_ion_refined0.079 | 0.2 | 3 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.223 | 0.2 | 35 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.078 | 0.2 | 9 | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined0.193 | 0.2 | 1 | X-RAY DIFFRACTION | r_mcbond_it1.055 | 1.5 | 636 | X-RAY DIFFRACTION | r_mcangle_it1.719 | 2 | 1002 | X-RAY DIFFRACTION | r_scbond_it2.654 | 3 | 525 | X-RAY DIFFRACTION | r_scangle_it4.21 | 4.5 | 460 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.939→1.989 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.291 | 35 | - |
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Rwork | 0.21 | 888 | - |
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all | - | 923 | - |
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obs | - | 923 | 100 % |
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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 | 6.5778 | 10.5485 | -0.4238 | 29.775 | -1.8641 | 13.0781 | -0.0646 | 0.0505 | -0.6663 | 0.4176 | -0.0185 | -3.1862 | 1.1081 | 1.1544 | 0.0831 | -0.0319 | 0.0136 | -0.071 | 0.0533 | -0.0314 | 0.1562 | 29.9447 | 17.7368 | 12.9412 | 2 | 0.603 | -1.8104 | -0.1635 | 6.3126 | 0.2153 | 0.1311 | 0.002 | 0.0443 | 0.0437 | 0.364 | 0.068 | -0.3234 | 0.0491 | -0.0028 | -0.07 | -0.0539 | -0.0043 | -0.0385 | -0.1115 | -0.01 | -0.0718 | 20.1522 | 31.3033 | 15.7684 | 3 | 0.8495 | -2.7999 | -1.5361 | 9.2471 | 5.2489 | 4.6235 | -0.028 | 0.0033 | -0.0039 | -0.1168 | 0.1061 | -0.4298 | 0.0031 | 0.0785 | -0.0782 | -0.0904 | -0.0096 | 0.009 | -0.1261 | -0.0134 | -0.0595 | 21.5517 | 36.8174 | 7.2711 | 4 | 3.2826 | 2.0604 | 0.9709 | 5.47 | -0.0302 | 0.3851 | 0.3225 | 0.0996 | 0.0217 | -0.0673 | -0.1521 | -0.2038 | -0.0122 | -0.0766 | -0.1704 | -0.059 | 0.0163 | 0.0156 | -0.0885 | -0.0003 | -0.1027 | 21.6973 | 26.7169 | 3.8653 | 5 | 3.5756 | 4.2653 | -0.1973 | 5.1094 | -0.1146 | 0.6948 | 0.2771 | 0.099 | 0.1643 | 0.1057 | -0.0766 | 0.0051 | 0.2044 | 0.0249 | -0.2004 | -0.0835 | -0.0156 | 0.0064 | -0.0814 | 0.0013 | -0.0721 | 19.921 | 17.4175 | 5.8623 | 6 | 3.0982 | -1.8678 | 1.5633 | 1.1262 | -0.9155 | 9.703 | 0.1722 | -0.0333 | -0.107 | 0.2806 | -0.1289 | 0.0988 | 0.0922 | 0.013 | -0.0433 | -0.1067 | -0.0328 | -0.0051 | -0.0968 | -0.0127 | -0.0516 | 12.3689 | 19.8085 | 5.3423 | 7 | 7.9257 | -0.827 | 1.719 | 14.621 | -3.4753 | 1.1202 | 0.2884 | 0.3374 | -0.5637 | -0.9045 | -0.2071 | -0.4349 | 0.359 | -0.0039 | -0.0812 | 0.0171 | -0.0173 | -0.0448 | -0.0643 | 0.0096 | -0.0851 | 12.92 | 35.3617 | 3.6346 | 8 | 0.7238 | 1.2962 | 0.7985 | 2.4456 | 1.0017 | 2.3534 | -0.0629 | -0.0567 | 0.128 | 0.1291 | 0.0434 | 0.2208 | 0.0621 | -0.0446 | 0.0195 | -0.1057 | 0.0271 | -0.0003 | -0.1111 | -0.0046 | -0.0594 | 10.4712 | 40.8008 | 13.2055 | 9 | 4.102 | -3.479 | 0.8533 | 11.695 | -3.2512 | 0.908 | -0.1883 | 0.0937 | -0.2994 | -0.2587 | 0.3229 | 0.3376 | 0.3275 | -0.4896 | -0.1346 | -0.1307 | -0.055 | 0.0013 | -0.0284 | -0.0497 | -0.0714 | 5.6986 | 29.232 | 9.8484 | 10 | 0.2523 | 0.0168 | -0.1346 | 2.6173 | 0.8439 | 3.0407 | 0.0453 | -0.079 | 0.1323 | 0.2502 | -0.0891 | 0.0411 | 0.3595 | -0.2564 | 0.0439 | -0.0085 | -0.0395 | 0.0059 | -0.1296 | 0.0031 | -0.106 | 14.9094 | 19.7288 | 16.8227 | 11 | 8.8714 | 0.8013 | -0.5306 | 6.9996 | 0.0578 | 1.7681 | 0.0534 | -0.3388 | 0.1329 | 0.6758 | 0.132 | -0.4057 | -0.1164 | -0.0498 | -0.1854 | 0.0051 | -0.0316 | -0.1001 | -0.1097 | -0.0117 | -0.1158 | 24.2522 | 12.0541 | 19.5328 | 12 | 56.4949 | -10.6591 | 41.0921 | 23.2512 | -7.9768 | 29.891 | -1.5257 | -6.5822 | 1.7101 | 4.9564 | 2.5395 | -0.7901 | 0.061 | -3.174 | -1.0138 | 1.1173 | 0.0263 | -0.1012 | 0.9633 | 0.1425 | 0.5481 | 27.185 | 12.0465 | 27.0384 | 13 | 6.2131 | -0.6679 | 2.1731 | 14.5244 | -5.5048 | 14.1291 | -0.2596 | -0.2501 | -0.1703 | 0.4685 | 0.2155 | 0.5934 | 0.1171 | -0.4978 | 0.0441 | -0.0124 | -0.1094 | 0.0901 | -0.0838 | -0.0523 | -0.1165 | 10.3891 | 29.3802 | 20.3273 |
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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 | AA77 - 87 | 15 - 25 | 2 | X-RAY DIFFRACTION | 2 | AA88 - 102 | 26 - 40 | 3 | X-RAY DIFFRACTION | 3 | AA103 - 110 | 41 - 48 | 4 | X-RAY DIFFRACTION | 4 | AA111 - 117 | 49 - 55 | 5 | X-RAY DIFFRACTION | 5 | AA118 - 123 | 56 - 61 | 6 | X-RAY DIFFRACTION | 6 | AA124 - 128 | 62 - 66 | 7 | X-RAY DIFFRACTION | 7 | AA129 - 137 | 67 - 75 | 8 | X-RAY DIFFRACTION | 8 | AA138 - 149 | 76 - 87 | 9 | X-RAY DIFFRACTION | 9 | AA150 - 160 | 88 - 98 | 10 | X-RAY DIFFRACTION | 10 | AA161 - 168 | 99 - 106 | 11 | X-RAY DIFFRACTION | 11 | AA169 - 177 | 107 - 115 | 12 | X-RAY DIFFRACTION | 12 | AA178 - 183 | 116 - 121 | 13 | X-RAY DIFFRACTION | 13 | AA184 - 195 | 122 - 133 | | | | | | | | | | | | | | | | | | | | | | | | | | |
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