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 | 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: 1.85→37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.006 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.129 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.22457 | 1677 | 5.1 % | RANDOM |
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Rwork | 0.18455 | - | - | - |
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all | 0.18647 | 31621 | - | - |
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obs | 0.18647 | 31491 | 99.59 % | - |
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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: 28.539 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.52 Å2 | 0.26 Å2 | 0 Å2 |
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2- | - | 0.52 Å2 | 0 Å2 |
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3- | - | - | -0.79 Å2 |
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Refine analyze | | Free | Obs |
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Luzzati coordinate error | 0.129 Å | 0.052 Å |
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Luzzati d res low | - | 6 Å |
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Luzzati sigma a | 0.5 Å | 0.34 Å |
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精密化ステップ | サイクル: LAST / 解像度: 1.85→37 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2621 | 0 | 0 | 316 | 2937 |
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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_d0.012 | 0.022 | 2681 | X-RAY DIFFRACTION | r_angle_refined_deg1.243 | 1.97 | 3625 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.088 | 5 | 341 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg34.357 | 22.735 | 117 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg13.624 | 15 | 444 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg19.017 | 15 | 24 | X-RAY DIFFRACTION | r_chiral_restr0.087 | 0.2 | 393 | X-RAY DIFFRACTION | r_gen_planes_refined0.005 | 0.02 | 2058 | X-RAY DIFFRACTION | r_nbd_refined0.197 | 0.2 | 1252 | X-RAY DIFFRACTION | r_nbtor_refined0.305 | 0.2 | 1851 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.163 | 0.2 | 256 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.196 | 0.2 | 103 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.2 | 0.2 | 44 | X-RAY DIFFRACTION | r_mcbond_it0.862 | 1.5 | 1746 | X-RAY DIFFRACTION | r_mcangle_it1.225 | 2 | 2716 | X-RAY DIFFRACTION | r_scbond_it2.319 | 3 | 1038 | X-RAY DIFFRACTION | r_scangle_it3.663 | 4.5 | 909 | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 1.85→1.898 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.284 | 134 | - |
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Rwork | 0.236 | 2307 | - |
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obs | - | 2307 | 99.75 % |
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精密化 TLS | 手法: refined / Origin x: 23.876 Å / Origin y: 77.065 Å / Origin z: 6.692 Å
| 11 | 12 | 13 | 21 | 22 | 23 | 31 | 32 | 33 |
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T | 0.0262 Å2 | -0.0069 Å2 | 0.0317 Å2 | - | -0.0159 Å2 | -0.0069 Å2 | - | - | -0.0477 Å2 |
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L | 0.2915 °2 | 0.048 °2 | 0.0762 °2 | - | 0.304 °2 | 0.0045 °2 | - | - | 0.277 °2 |
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S | 0.0048 Å ° | -0.0119 Å ° | -0.0233 Å ° | 0.0242 Å ° | 0.0002 Å ° | 0.0467 Å ° | -0.0338 Å ° | -0.0319 Å ° | -0.0051 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 | AA-5 - 50 | 1 - 56 | 2 | X-RAY DIFFRACTION | 1 | AA51 - 100 | 57 - 106 | 3 | X-RAY DIFFRACTION | 1 | AA101 - 150 | 107 - 156 | 4 | X-RAY DIFFRACTION | 1 | AA151 - 200 | 157 - 206 | 5 | X-RAY DIFFRACTION | 1 | AA201 - 250 | 207 - 256 | 6 | X-RAY DIFFRACTION | 1 | AA251 - 300 | 257 - 306 | 7 | X-RAY DIFFRACTION | 1 | AA301 - 336 | 307 - 342 | | | | | | | | | | | | | | |
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