ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.3.0037精密化 | MAR345 | | データ収集 | DENZO | | データ削減 | SCALEPACK | | データスケーリング | REFMAC | | 位相決定 | |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: PDB ENTRY 1R5D 解像度: 1.6→27.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.041 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.092 / 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 | 0.20363 | 1575 | 5.1 % | RANDOM |
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Rwork | 0.17667 | - | - | - |
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obs | 0.17809 | 29510 | 97.64 % | - |
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all | - | 31120 | - | - |
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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 mean: 13.69 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.03 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.2 Å2 | 0 Å2 |
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3- | - | - | 0.17 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.197 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.6→27.6 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1882 | 0 | 42 | 309 | 2233 |
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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 | 0.022 | 1972 | X-RAY DIFFRACTION | r_angle_refined_deg1.342 | 1.971 | 2661 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.542 | 5 | 246 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg37.209 | 24.865 | 74 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg11.618 | 15 | 365 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg8.804 | 15 | 8 | X-RAY DIFFRACTION | r_chiral_restr0.09 | 0.2 | 295 | X-RAY DIFFRACTION | r_gen_planes_refined0.003 | 0.02 | 1420 | X-RAY DIFFRACTION | r_nbd_refined0.187 | 0.2 | 940 | X-RAY DIFFRACTION | r_nbtor_refined0.289 | 0.2 | 1349 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.117 | 0.2 | 242 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.15 | 0.2 | 62 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.11 | 0.2 | 35 | X-RAY DIFFRACTION | r_mcbond_it0.512 | 1.5 | 1275 | X-RAY DIFFRACTION | r_mcangle_it0.895 | 2 | 2013 | X-RAY DIFFRACTION | r_scbond_it1.485 | 3 | 775 | X-RAY DIFFRACTION | r_scangle_it2.394 | 4.5 | 648 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.597→1.638 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.25 | 95 | - |
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Rwork | 0.193 | 1863 | - |
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obs | - | - | 85.61 % |
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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 | 5.6273 | 0.3354 | -1.7783 | 2.2686 | 0.6301 | 6.8477 | 0.1049 | -0.4449 | -0.0008 | 0.2967 | -0.1246 | -0.0855 | 0.0777 | 0.3938 | 0.0197 | 0.0476 | -0.0312 | -0.0059 | 0.0648 | 0.0011 | -0.0067 | 11.11 | 19.4628 | 23.2601 | 2 | 6.2776 | -2.6229 | 0.9468 | 7.4824 | -3.8659 | 3.7598 | 0.2164 | 0.4075 | 0.3185 | -0.4804 | -0.0999 | 0.0535 | 0.1247 | 0.0244 | -0.1165 | 0.049 | 0.0052 | -0.0019 | 0.043 | 0.0031 | 0.0203 | 7.0092 | 22.6078 | 9.518 | 3 | 3.3837 | 1.0092 | -0.0998 | 1.9527 | -0.7547 | 2.1474 | 0.03 | 0.1027 | 0.0731 | -0.1485 | 0.0244 | 0.2625 | 0.0783 | -0.1692 | -0.0544 | 0.0033 | -0.0068 | -0.0055 | 0.0178 | -0.0071 | 0.0515 | 18.683 | 27.345 | 5.475 | 4 | 14.4668 | -6.0402 | -7.1881 | 10.2616 | 12.4493 | 15.1052 | 0.1109 | -0.9287 | 0.195 | 1.0315 | -0.0782 | 0.042 | 0.1596 | -0.1091 | -0.0327 | 0.0789 | -0.0166 | 0.0154 | 0.1017 | -0.0333 | -0.035 | 23.8376 | 32.0735 | 16.7223 | 5 | 2.6859 | 0.383 | -0.7074 | 1.2172 | 0.258 | 1.2722 | 0.0264 | 0.0554 | 0.0107 | -0.0435 | -0.0038 | -0.0156 | -0.0402 | -0.0082 | -0.0226 | 0.0572 | 0.0029 | -0.0131 | 0.0228 | -0.0032 | 0.0452 | 34.6896 | 31.4998 | 1.2953 | 6 | 0.7861 | 0.489 | 0.1871 | 5.3067 | 4.5374 | 7.4397 | 0.0745 | 0.0077 | -0.01 | -0.2051 | 0.1082 | -0.1759 | -0.349 | 0.0002 | -0.1827 | 0.0618 | -0.0209 | 0.009 | 0.0063 | 0.0053 | 0.033 | 42.5822 | 42.747 | 2.5107 | 7 | 9.8052 | 1.427 | -3.5671 | 3.2679 | -0.9192 | 4.6238 | -0.0617 | 0.4148 | 0.0155 | -0.2731 | 0.1443 | -0.007 | 0.1936 | 0.1059 | -0.0826 | 0.0811 | 0.0025 | -0.0285 | 0.0523 | -0.0004 | 0.0249 | 31.8979 | 33.5222 | -5.6141 | 8 | 4.0505 | -0.5556 | -1.3197 | 1.4793 | -2.1846 | 7.8655 | 0.0903 | -0.4232 | 0.3217 | 0.3418 | 0.1454 | 0.5111 | -0.5136 | -0.6559 | -0.2357 | -0.0126 | 0.0176 | 0.0737 | 0.024 | -0.0578 | 0.1142 | 15.8879 | 37.958 | 11.8618 | 9 | 4.9414 | 0.8065 | -2.1649 | 0.6077 | -0.711 | 3.0583 | -0.0483 | 0.2488 | 0.2371 | -0.0961 | 0.07 | 0.2147 | -0.0243 | -0.1181 | -0.0217 | 0.0745 | 0.0157 | -0.0281 | 0.0088 | 0.0147 | 0.0861 | 24.6469 | 35.7905 | -1.9507 | 10 | 4.9204 | -3.3742 | 2.4493 | 4.5127 | -1.6342 | 3.0221 | -0.0682 | -0.0475 | 0.1023 | -0.0301 | 0.0818 | -0.0559 | -0.0751 | -0.0233 | -0.0136 | 0.0449 | -0.0165 | -0.0112 | 0.0234 | 0.0101 | 0.0387 | 40.4735 | 35.6662 | 4.9837 | 11 | 9.327 | 0.8149 | -0.4229 | 2.3177 | -1.1896 | 4.2501 | 0.0512 | -0.6908 | -0.117 | 0.2733 | -0.2179 | -0.0975 | -0.1143 | 0.1589 | 0.1666 | 0.0323 | -0.0186 | -0.0154 | 0.0491 | 0.024 | 0.0143 | 35.9517 | 28.7526 | 12.4712 | 12 | 1.5402 | 1.2578 | -0.5272 | 1.0279 | -0.4153 | 0.5174 | -0.1273 | 0.2668 | -0.0805 | -0.0648 | 0.1223 | 0.0314 | 0.0451 | -0.0789 | 0.005 | 0.0215 | -0.007 | 0.0074 | 0.0294 | -0.0137 | 0.0386 | 23.2385 | 22.764 | 1.0792 | 13 | 0.9995 | 0.4295 | -0.4725 | 1.9384 | -0.4447 | 1.7531 | 0.0877 | 0.0029 | 0.0188 | -0.1311 | 0.0061 | -0.147 | -0.0254 | 0.0198 | -0.0938 | -0.0009 | -0.0025 | 0.0085 | 0.0436 | -0.0099 | 0.0515 | 18.7707 | 20.383 | 11.0035 | 14 | 19.2138 | -14.5842 | 0.4881 | 12.5676 | -3.8792 | 8.2332 | -0.1248 | -0.6829 | -0.0983 | 0.8532 | 0.141 | -0.9213 | -0.0484 | 0.8757 | -0.0162 | 0.007 | 0.0187 | -0.0921 | 0.1104 | -0.0024 | 0.0543 | 22.7732 | 15.9186 | 17.8089 | 15 | 1.9788 | -0.1816 | -0.0942 | 1.2862 | -0.3518 | 1.5018 | 0.0485 | -0.0236 | -0.0395 | 0.0248 | -0.0118 | 0.0467 | 0.0708 | -0.0686 | -0.0367 | 0.0521 | 0.0008 | -0.0055 | 0.0355 | -0.0052 | 0.04 | 3.6752 | 16.2585 | 14.5137 | 16 | 12.0046 | -7.5717 | 8.2453 | 11.5696 | -7.5385 | 6.4677 | 0.0141 | -0.1005 | -0.4137 | -0.1784 | 0.331 | 0.3862 | 0.1896 | -0.0214 | -0.3451 | 0.0527 | -0.0221 | -0.0073 | 0.065 | 0.0221 | -0.0002 | 0.5204 | 2.9993 | 20.843 | 17 | 1.2166 | 0.3997 | -0.4557 | 1.3622 | -1.0039 | 1.7544 | 0.0214 | 0.0053 | -0.054 | -0.0311 | 0.0463 | 0.052 | 0.096 | -0.0926 | -0.0678 | 0.0797 | -0.0012 | -0.0152 | 0.0454 | -0.014 | 0.0399 | 3.0019 | 11.0204 | 12.9922 | 18 | 12.7497 | 4.6827 | 13.321 | 13.0001 | 9.8273 | 22.0604 | 0.1482 | 0.6364 | -0.3206 | -0.5301 | -0.1998 | -1.144 | -0.1735 | 1.7418 | 0.0515 | -0.0663 | 0.0824 | 0.0729 | 0.1218 | 0.0802 | 0.116 | 28.0252 | 10.1262 | 9.4733 | 19 | 6.423 | 0.4046 | -1.1295 | 0.2256 | -0.1874 | 1.6737 | -0.1265 | 0.3615 | 0.0471 | -0.0511 | 0.1009 | -0.0786 | 0.1733 | -0.0785 | 0.0256 | 0.0973 | 0.011 | 0.004 | 0.0312 | -0.0172 | 0.0564 | 8.949 | 12.035 | 5.0976 | 20 | 1.2848 | -0.8978 | -1.123 | 2.9186 | 2.9842 | 6.5785 | 0.0596 | -0.0474 | -0.0712 | 0.0471 | 0.0347 | -0.0086 | 0.1123 | -0.0282 | -0.0943 | 0.0542 | -0.0053 | 0.0059 | 0.04 | 0.0022 | 0.0148 | 2.3408 | 12.6476 | 20.8883 |
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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 | AA1 - 11 | 1 - 11 | 2 | X-RAY DIFFRACTION | 2 | AA12 - 18 | 12 - 18 | 3 | X-RAY DIFFRACTION | 3 | AA19 - 33 | 19 - 33 | 4 | X-RAY DIFFRACTION | 4 | AA34 - 39 | 34 - 39 | 5 | X-RAY DIFFRACTION | 5 | AA40 - 60 | 40 - 60 | 6 | X-RAY DIFFRACTION | 6 | AA61 - 75 | 61 - 75 | 7 | X-RAY DIFFRACTION | 7 | AA76 - 83 | 76 - 83 | 8 | X-RAY DIFFRACTION | 8 | AA84 - 95 | 84 - 95 | 9 | X-RAY DIFFRACTION | 9 | AA96 - 106 | 96 - 106 | 10 | X-RAY DIFFRACTION | 10 | AA107 - 124 | 107 - 124 | 11 | X-RAY DIFFRACTION | 11 | BB1 - 11 | 1 - 11 | 12 | X-RAY DIFFRACTION | 12 | BB12 - 26 | 12 - 26 | 13 | X-RAY DIFFRACTION | 13 | BB27 - 33 | 27 - 33 | 14 | X-RAY DIFFRACTION | 14 | BB34 - 39 | 34 - 39 | 15 | X-RAY DIFFRACTION | 15 | BB40 - 61 | 40 - 61 | 16 | X-RAY DIFFRACTION | 16 | BB62 - 68 | 62 - 68 | 17 | X-RAY DIFFRACTION | 17 | BB69 - 86 | 69 - 86 | 18 | X-RAY DIFFRACTION | 18 | BB87 - 95 | 87 - 95 | 19 | X-RAY DIFFRACTION | 19 | BB96 - 106 | 96 - 106 | 20 | X-RAY DIFFRACTION | 20 | BB107 - 124 | 107 - 124 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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