ソフトウェア | 名称 | バージョン | 分類 |
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ADSC | Quantumデータ収集 | MOLREP | | 位相決定 | REFMAC | 5.5.0088精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: Swiss Model 解像度: 2.09→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.926 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.186 / 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 | 0.24 | 2782 | 5.1 % | RANDOM |
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Rwork | 0.192 | - | - | - |
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obs | 0.195 | 54799 | - | - |
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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: 21.03 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -0.56 Å2 | 0 Å2 | 0.14 Å2 |
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2- | - | 1.23 Å2 | 0 Å2 |
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3- | - | - | -0.64 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.09→50 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6529 | 0 | 0 | 340 | 6869 |
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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_d0.011 | 0.022 | 6590 | X-RAY DIFFRACTION | r_bond_other_d0.002 | 0.02 | 4427 | X-RAY DIFFRACTION | r_angle_refined_deg1.164 | 1.957 | 8850 | X-RAY DIFFRACTION | r_angle_other_deg0.868 | 3 | 10803 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.296 | 5 | 857 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg36.662 | 23.962 | 265 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.562 | 15 | 1198 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg16.028 | 15 | 48 | X-RAY DIFFRACTION | r_chiral_restr0.068 | 0.2 | 1045 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 7319 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1297 | 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_it0.716 | 1.5 | 4272 | X-RAY DIFFRACTION | r_mcbond_other0.169 | 1.5 | 1813 | X-RAY DIFFRACTION | r_mcangle_it1.361 | 2 | 6770 | X-RAY DIFFRACTION | r_scbond_it1.97 | 3 | 2318 | X-RAY DIFFRACTION | r_scangle_it3.3 | 4.5 | 2080 | X-RAY DIFFRACTION | r_rigid_bond_restr | | | X-RAY DIFFRACTION | r_sphericity_free | | | X-RAY DIFFRACTION | r_sphericity_bonded | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION Auth asym-ID | 数 | タイプ | Rms dev position (Å) | Weight position |
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A1208 | medium positional0.29 | 0.5 | B1208 | medium positional0.62 | 0.5 | C1208 | medium positional0.31 | 0.5 | D1208 | medium positional0.27 | 0.5 | A1356 | loose positional0.7 | 5 | B1356 | loose positional1.12 | 5 | C1356 | loose positional0.76 | 5 | D1356 | loose positional0.66 | 5 | A1208 | medium thermal0.6 | 2 | B1208 | medium thermal0.53 | 2 | C1208 | medium thermal0.48 | 2 | D1208 | medium thermal0.49 | 2 | A1356 | loose thermal0.57 | 10 | B1356 | loose thermal0.55 | 10 | C1356 | loose thermal0.53 | 10 | D1356 | loose thermal0.49 | 10 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.09→2.14 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.263 | 171 | - |
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Rwork | 0.218 | 3556 | - |
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obs | - | - | 91.57 % |
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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 | 0.964 | 0.1802 | -0.0539 | 1.1536 | 0.3026 | 0.4832 | -0.0296 | -0.1103 | 0.061 | 0.0061 | -0.0649 | 0.1318 | 0.0717 | -0.0922 | 0.0945 | 0.0367 | 0.0118 | 0.0245 | 0.1011 | -0.0101 | 0.0357 | 1.377 | -1.995 | 46.651 | 2 | 0.8429 | -0.2501 | -0.4145 | 0.6455 | -0.2433 | 1.8067 | 0.0915 | 0.028 | 0.1487 | -0.0556 | -0.093 | -0.1193 | -0.2332 | 0.1215 | 0.0014 | 0.0899 | -0.0448 | -0.0064 | 0.0653 | 0.027 | 0.0779 | 23.123 | 13.497 | 32.32 | 3 | 1.3186 | 0.254 | -0.8821 | 1.1922 | 0.5093 | 1.8788 | 0.0444 | 0.15 | -0.0215 | -0.0381 | -0.0367 | -0.1275 | -0.0235 | -0.2023 | -0.0078 | 0.0468 | 0.0335 | 0.0126 | 0.1585 | 0.0069 | 0.0176 | 24.971 | -11.782 | 9.379 | 4 | 2.5261 | 0.0352 | -1.3068 | 0.9071 | 0.0921 | 1.9952 | -0.1783 | 0.5102 | -0.3885 | -0.0062 | -0.0569 | 0.0709 | 0.271 | -0.4301 | 0.2352 | 0.1101 | -0.1095 | 0.0225 | 0.1874 | -0.117 | 0.1406 | 0.993 | -25.095 | 21.461 |
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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 - 242 | 2 | X-RAY DIFFRACTION | 2 | B0 - 244 | 3 | X-RAY DIFFRACTION | 3 | C0 - 243 | 4 | X-RAY DIFFRACTION | 4 | D0 - 243 | | | | |
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