ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.2.0019精密化 | SBC-Collect | | データ収集 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | HKL-3000 | | 位相決定 | SHELXE | | モデル構築 | SOLVE | | 位相決定 | RESOLVE | | 位相決定 | ARP/wARP | | モデル構築 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.19→44.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.673 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.222 / ESU R Free: 0.198 / 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 | 0.2469 | 635 | 4.9 % | RANDOM |
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Rwork | 0.1913 | - | - | - |
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obs | 0.1939 | 12388 | 99.43 % | - |
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all | - | 12463 | - | - |
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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: 37.136 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 1.18 Å2 | 0 Å2 | 0 Å2 |
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2- | - | -0.34 Å2 | 0 Å2 |
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3- | - | - | -0.84 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.042 Å | 0.035 Å |
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Luzzati d res low | - | 6 Å |
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Luzzati sigma a | 0.5 Å | 0.32 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.19→44.7 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1474 | 0 | 6 | 127 | 1607 |
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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 | 0.021 | 1501 | X-RAY DIFFRACTION | r_angle_refined_deg1.289 | 1.969 | 2031 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg4.972 | 5 | 192 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg33.138 | 22.676 | 71 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.561 | 15 | 251 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg18.117 | 15 | 19 | X-RAY DIFFRACTION | r_chiral_restr0.094 | 0.2 | 227 | X-RAY DIFFRACTION | r_gen_planes_refined0.004 | 0.02 | 1148 | X-RAY DIFFRACTION | r_nbd_refined0.216 | 0.2 | 722 | X-RAY DIFFRACTION | r_nbtor_refined0.296 | 0.2 | 1043 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.178 | 0.2 | 107 | X-RAY DIFFRACTION | r_metal_ion_refined0.02 | 0.2 | 1 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.171 | 0.2 | 67 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.181 | 0.2 | 26 | X-RAY DIFFRACTION | r_symmetry_metal_ion_refined0.479 | 0.2 | 2 | X-RAY DIFFRACTION | r_mcbond_it0.717 | 1.5 | 986 | X-RAY DIFFRACTION | r_mcangle_it1.219 | 2 | 1509 | X-RAY DIFFRACTION | r_scbond_it2.351 | 3 | 578 | X-RAY DIFFRACTION | r_scangle_it3.836 | 4.5 | 522 | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.19→2.25 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.325 | 34 | - |
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Rwork | 0.21 | 824 | - |
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obs | - | 858 | 92.86 % |
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精密化 TLS | 手法: refined / Origin x: 13.043 Å / Origin y: 29.706 Å / Origin z: 30.002 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | -0.1146 Å2 | -0.0102 Å2 | 0.0107 Å2 | - | -0.0966 Å2 | 0.0107 Å2 | - | - | -0.1208 Å2 |
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L | 0.6923 °2 | 0.0857 °2 | -0.0582 °2 | - | 1.8241 °2 | 0.1885 °2 | - | - | 2.7763 °2 |
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S | 0.0523 Å ° | 0.1832 Å ° | 0.0588 Å ° | 0.1456 Å ° | -0.0702 Å ° | 0.0001 Å ° | 0.308 Å ° | -0.0421 Å ° | 0.0179 Å ° |
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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 | AA9 - 50 | 9 - 50 | 2 | X-RAY DIFFRACTION | 1 | AA51 - 100 | 51 - 100 | 3 | X-RAY DIFFRACTION | 1 | AA101 - 150 | 101 - 150 | 4 | X-RAY DIFFRACTION | 1 | AA151 - 200 | 151 - 200 | | | | | | | | |
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