ソフトウェア | 名称 | バージョン | 分類 |
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SBC-Collect | | データ収集 | HKL-3000 | | 位相決定 | SHELXD | | 位相決定 | SHELXE | | モデル構築 | MLPHARE | | 位相決定 | 直接法 | | モデル構築 | RESOLVE | | モデル構築 | Coot | | モデル構築 | ARP/wARP | | モデル構築 | REFMAC | 5.5.0102精密化 | HKL-3000 | | データ削減 | HKL-3000 | | データスケーリング | 直接法 | | 位相決定 | RESOLVE | | 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: 1.45→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.384 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072 / 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 | 0.19198 | 2660 | 5.1 % | RANDOM |
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Rwork | 0.16426 | - | - | - |
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all | 0.16567 | 52205 | - | - |
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obs | 0.16567 | 52205 | 98.62 % | - |
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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: 1.4 Å / 溶媒モデル: MASK |
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原子変位パラメータ | Biso mean: 11.755 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.1 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 0.27 Å2 | 0 Å2 |
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3- | - | - | -0.37 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.45→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2493 | 0 | 6 | 480 | 2979 |
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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_d0.014 | 0.021 | 2805 | X-RAY DIFFRACTION | r_bond_other_d | | | X-RAY DIFFRACTION | r_angle_refined_deg1.467 | 1.926 | 3880 | X-RAY DIFFRACTION | r_angle_other_deg | | | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.96 | 5 | 363 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.936 | 23.185 | 135 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg10.795 | 15 | 394 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg20.372 | 15 | 21 | X-RAY DIFFRACTION | r_chiral_restr0.091 | 0.2 | 424 | X-RAY DIFFRACTION | r_gen_planes_refined0.009 | 0.022 | 2291 | X-RAY DIFFRACTION | r_gen_planes_other | | | X-RAY DIFFRACTION | r_nbd_refined | | | X-RAY DIFFRACTION | r_nbd_other | | | X-RAY DIFFRACTION | r_nbtor_refined | | | X-RAY DIFFRACTION | r_nbtor_other | | | X-RAY DIFFRACTION | r_xyhbond_nbd_refined | | | X-RAY DIFFRACTION | r_xyhbond_nbd_other | | | X-RAY DIFFRACTION | r_metal_ion_refined | | | X-RAY DIFFRACTION | r_metal_ion_other | | | X-RAY DIFFRACTION | r_symmetry_vdw_refined | | | X-RAY DIFFRACTION | r_symmetry_vdw_other | | | X-RAY DIFFRACTION | r_symmetry_hbond_refined | | | X-RAY DIFFRACTION | r_symmetry_hbond_other | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined | | | X-RAY DIFFRACTION | r_symmetry_metal_ion_other | | | X-RAY DIFFRACTION | r_mcbond_it0.825 | 1.5 | 1746 | X-RAY DIFFRACTION | r_mcbond_other | | | X-RAY DIFFRACTION | r_mcangle_it1.441 | 2 | 2884 | X-RAY DIFFRACTION | r_scbond_it2.193 | 3 | 1059 | X-RAY DIFFRACTION | r_scangle_it3.35 | 4.5 | 996 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.45→1.488 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.267 | 148 | - |
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Rwork | 0.229 | 3246 | - |
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obs | - | 3394 | 87.97 % |
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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 | 1.3502 | 0.6291 | -0.8543 | 0.8639 | -0.4273 | 1.4765 | 0.0079 | 0.0048 | 0.004 | -0.0527 | 0.0286 | -0.0037 | 0.1512 | 0.0077 | -0.0365 | 0.0376 | 0.007 | -0.0138 | 0.0211 | -0.0108 | 0.0125 | 17.8422 | 17.4352 | 10.1763 | 2 | 2.1382 | 0.3824 | 0.3931 | 0.8526 | -0.0134 | 0.5235 | -0.0777 | -0.0195 | 0.2687 | -0.033 | 0.0314 | -0.0798 | -0.0124 | 0.0361 | 0.0463 | 0.0156 | 0.0073 | -0.0103 | 0.0122 | -0.0115 | 0.0566 | 28.3039 | 32.9221 | 7.6098 | 3 | 2.3799 | 3.1003 | 0.5391 | 4.8265 | 0.115 | 0.58 | 0.054 | -0.1652 | 0.1818 | 0.1406 | -0.0601 | 0.3015 | -0.0299 | -0.1055 | 0.0062 | 0.0799 | 0.0314 | 0.0076 | 0.1456 | -0.0038 | 0.1492 | 9.7612 | 41.1777 | 6.606 | 4 | 0.2084 | 0.4141 | 0.0025 | 1.5181 | 0.233 | 0.6282 | -0.0428 | -0.0209 | 0.0093 | -0.1078 | 0.0252 | -0.0331 | -0.0701 | -0.0579 | 0.0177 | 0.0367 | 0.0099 | -0.0239 | 0.0276 | -0.0039 | 0.0302 | 17.4188 | 38.0991 | 1.5481 | 5 | 1.7365 | 1.4077 | -0.1242 | 7.1032 | 0.4571 | 1.1012 | -0.0239 | 0.0658 | 0.1343 | -0.476 | 0.0752 | -0.2048 | -0.1048 | 0.0946 | -0.0513 | 0.0402 | -0.0091 | 0.0221 | 0.028 | 0.0003 | 0.0282 | 26.0441 | 34.1096 | -3.5916 | 6 | 0.4347 | 0.187 | 0.1094 | 0.5809 | -0.1362 | 0.5746 | 0.0018 | -0.002 | 0.0289 | -0.0481 | 0.0332 | -0.0311 | 0.1764 | 0.0412 | -0.0349 | 0.0599 | 0.0098 | -0.0064 | 0.0376 | -0.0131 | 0.0397 | 24.0413 | 18.2478 | 11.7813 | 7 | 1.1678 | -0.4441 | -0.2116 | 0.1899 | 0.1056 | 0.5442 | -0.0037 | -0.0758 | -0.0423 | 0.0043 | -0.0027 | 0.0305 | 0.0779 | -0.048 | 0.0064 | 0.0289 | -0.0122 | -0.0087 | 0.0599 | -0.008 | 0.0232 | 5.6842 | 21.6357 | 21.71 | 8 | 5.2049 | -2.9503 | -3.1352 | 1.677 | 1.7648 | 2.7121 | 0.3528 | 0.1246 | 0.4512 | -0.1729 | -0.0396 | -0.2355 | -0.2494 | 0.0386 | -0.3132 | 0.1307 | 0.0191 | 0.0784 | 0.0879 | 0.0098 | 0.2187 | 18.0663 | 36.6592 | 29.2909 | 9 | 0.8063 | -0.0712 | -0.3175 | 0.637 | 0.2038 | 0.9704 | 0.0353 | 0.0381 | 0.0618 | 0.0594 | -0.0194 | 0.0205 | 0.0121 | -0.0996 | -0.0159 | 0.0283 | 0.0079 | -0.0062 | 0.0304 | -0.0005 | 0.0126 | 14.2581 | 27.3706 | 30.6589 | 10 | 2.2033 | -0.9193 | -1.492 | 1.6135 | 0.8136 | 1.8853 | -0.0832 | -0.1249 | -0.0659 | 0.1402 | 0.0434 | 0.0476 | 0.2305 | -0.0782 | 0.0398 | 0.053 | -0.023 | -0.004 | 0.0513 | 0.0058 | 0.0068 | 9.7188 | 17.1488 | 31.3239 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | A0 - 23 | 2 | X-RAY DIFFRACTION | 2 | A24 - 59 | 3 | X-RAY DIFFRACTION | 3 | A60 - 77 | 4 | X-RAY DIFFRACTION | 4 | A78 - 136 | 5 | X-RAY DIFFRACTION | 5 | A137 - 157 | 6 | X-RAY DIFFRACTION | 6 | B0 - 23 | 7 | X-RAY DIFFRACTION | 7 | B24 - 59 | 8 | X-RAY DIFFRACTION | 8 | B60 - 77 | 9 | X-RAY DIFFRACTION | 9 | B78 - 136 | 10 | X-RAY DIFFRACTION | 10 | B137 - 157 | | | | | | | | | | |
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