ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | PHASER | | 位相決定 | | REFMAC | | 精密化 | | PDB_EXTRACT | 3 | データ抽出 | | BOS | | データ収集 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: CRYSTAL STRUCTURE OF CCML PDB ID 2QW7 解像度: 2.15→43.4 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.751 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.223 / 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 | 0.243 | 1022 | 5.1 % | RANDOM |
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Rwork | 0.184 | - | - | - |
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obs | 0.187 | 20042 | 99.32 % | - |
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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: 13.161 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.06 Å2 | 0 Å2 | -0.02 Å2 |
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2- | - | 0.03 Å2 | 0 Å2 |
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3- | - | - | -0.09 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.15→43.4 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 3015 | 0 | 19 | 267 | 3301 |
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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_d0.006 | 0.022 | 3088 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 2081 | X-RAY DIFFRACTION | r_angle_refined_deg1.001 | 1.967 | 4192 | X-RAY DIFFRACTION | r_angle_other_deg0.777 | 3 | 5132 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg5.677 | 5 | 399 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg32.59 | 24.653 | 101 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.708 | 15 | 530 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg11.479 | 15 | 15 | X-RAY DIFFRACTION | r_chiral_restr0.054 | 0.2 | 488 | X-RAY DIFFRACTION | r_gen_planes_refined0.002 | 0.02 | 3351 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 534 | X-RAY DIFFRACTION | r_nbd_refined0.204 | 0.2 | 528 | X-RAY DIFFRACTION | r_nbd_other0.186 | 0.2 | 2218 | X-RAY DIFFRACTION | r_nbtor_refined0.163 | 0.2 | 1443 | X-RAY DIFFRACTION | r_nbtor_other0.082 | 0.2 | 1654 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.116 | 0.2 | 211 | X-RAY DIFFRACTION | r_symmetry_vdw_refined0.222 | 0.2 | 10 | X-RAY DIFFRACTION | r_symmetry_vdw_other0.229 | 0.2 | 41 | X-RAY DIFFRACTION | r_symmetry_hbond_refined0.132 | 0.2 | 23 | X-RAY DIFFRACTION | r_mcbond_it1.282 | 2 | 2155 | X-RAY DIFFRACTION | r_mcbond_other0.249 | 2 | 814 | X-RAY DIFFRACTION | r_mcangle_it1.795 | 3 | 3237 | X-RAY DIFFRACTION | r_scbond_it1.168 | 2 | 1221 | X-RAY DIFFRACTION | r_scangle_it1.652 | 3 | 955 | | | | | | | | | | | | | | | | | | | | | | | | |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION Dom-ID | Auth asym-ID | 数 | タイプ | Rms dev position (Å) | Weight position |
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1 | A402 | MEDIUM POSITIONAL0.12 | 0.5 | 2 | B402 | MEDIUM POSITIONAL0.1 | 0.5 | 3 | C402 | MEDIUM POSITIONAL0.12 | 0.5 | 4 | D402 | MEDIUM POSITIONAL0.2 | 0.5 | 5 | E402 | MEDIUM POSITIONAL0.14 | 0.5 | 1 | A132 | LOOSE POSITIONAL0.44 | 5 | 2 | B132 | LOOSE POSITIONAL0.57 | 5 | 3 | C132 | LOOSE POSITIONAL0.37 | 5 | 4 | D132 | LOOSE POSITIONAL0.42 | 5 | 5 | E132 | LOOSE POSITIONAL0.34 | 5 | 1 | A402 | MEDIUM THERMAL0.42 | 2 | 2 | B402 | MEDIUM THERMAL0.32 | 2 | 3 | C402 | MEDIUM THERMAL0.34 | 2 | 4 | D402 | MEDIUM THERMAL0.31 | 2 | 5 | E402 | MEDIUM THERMAL0.38 | 2 | 1 | A132 | LOOSE THERMAL2.74 | 10 | 2 | B132 | LOOSE THERMAL1.1 | 10 | 3 | C132 | LOOSE THERMAL0.94 | 10 | 4 | D132 | LOOSE THERMAL0.99 | 10 | 5 | E132 | LOOSE THERMAL1.4 | 10 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.155→2.21 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.26 | 73 | - |
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Rwork | 0.209 | 1322 | - |
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all | - | 1395 | - |
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obs | - | - | 93.44 % |
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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 | 1.7697 | -0.4401 | -0.5396 | 3.2659 | 0.8177 | 1.9804 | 0.0554 | -0.0643 | -0.0293 | -0.0746 | -0.0745 | -0.1261 | 0.0001 | 0.0836 | 0.0191 | -0.068 | 0.0042 | -0.0154 | -0.0368 | 0.0022 | -0.0145 | -0.5635 | -13.4671 | -5.9275 | 2 | 3.0059 | 0.1868 | 0.4619 | 1.1233 | 0.6371 | 1.8983 | -0.0309 | 0.0051 | -0.1201 | -0.0202 | 0.0171 | -0.0124 | 0.1163 | -0.0912 | 0.0138 | -0.0292 | -0.0201 | -0.0044 | -0.0808 | 0.0195 | -0.0471 | -17.2907 | -22.2867 | -5.3833 | 3 | 0.9213 | -0.5115 | 0.116 | 2.4915 | -0.1728 | 1.81 | -0.0293 | 0.0252 | -0.0053 | -0.0538 | 0.0287 | 0.186 | -0.1016 | -0.2158 | 0.0006 | -0.071 | -0.0236 | 0.0022 | 0.0009 | 0.0161 | -0.0196 | -31.8576 | -9.229 | -5.411 | 4 | 1.4109 | 0.7279 | -0.0438 | 2.151 | -0.8366 | 2.1718 | -0.0008 | -0.0015 | 0.0841 | -0.0313 | 0.0088 | 0.0888 | -0.0408 | -0.1192 | -0.008 | -0.0275 | 0.0467 | 0.0111 | -0.0494 | -0.0201 | -0.0438 | -24.5136 | 8.3403 | -4.9872 | 5 | 2.5844 | -0.2643 | -1.0472 | 1.0102 | 0.6997 | 2.349 | -0.0149 | 0.0194 | -0.0119 | -0.0563 | 0.0255 | -0.0519 | -0.0526 | 0.1553 | -0.0106 | -0.031 | -0.0347 | -0.0171 | -0.0583 | -0.0137 | -0.0333 | -4.7014 | 7.0592 | -5.3644 |
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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 - 82 | 1 - 82 | 2 | X-RAY DIFFRACTION | 2 | BB1 - 81 | 1 - 81 | 3 | X-RAY DIFFRACTION | 3 | CC1 - 81 | 1 - 81 | 4 | X-RAY DIFFRACTION | 4 | DD1 - 80 | 1 - 80 | 5 | X-RAY DIFFRACTION | 5 | EE1 - 80 | 1 - 80 | | | | | | | | | | |
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