ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALEPACK | | データスケーリング | | PHASER | | 位相決定 | | REFMAC | | 精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | CBASS | | データ収集 | | HKL-2000 | | データ削減 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 1S69 解像度: 2.25→34.19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.2914 / WRfactor Rwork: 0.2215 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7737 / SU B: 14.864 / SU ML: 0.228 / SU R Cruickshank DPI: 0.3919 / SU Rfree: 0.2782 / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.392 / ESU R Free: 0.278 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2881 | 609 | 5 % | RANDOM |
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Rwork | 0.2179 | - | - | - |
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all | 0.2214 | 12279 | - | - |
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obs | 0.2214 | 12279 | 99.8 % | - |
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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 max: 106.81 Å2 / Biso mean: 46.3993 Å2 / Biso min: 20.87 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.45 Å2 | 0 Å2 | 1.32 Å2 |
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2- | - | -1.16 Å2 | -0 Å2 |
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3- | - | - | 0.15 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.25→34.19 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1934 | 0 | 105 | 37 | 2076 |
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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_d0.013 | 0.019 | 2080 | X-RAY DIFFRACTION | r_bond_other_d0.007 | 0.02 | 1944 | X-RAY DIFFRACTION | r_angle_refined_deg1.7 | 2.007 | 2832 | X-RAY DIFFRACTION | r_angle_other_deg0.754 | 3 | 4422 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.634 | 5 | 244 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg39.568 | 24.717 | 106 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg15.368 | 15 | 336 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.202 | 15 | 14 | X-RAY DIFFRACTION | r_chiral_restr0.06 | 0.2 | 303 | X-RAY DIFFRACTION | r_gen_planes_refined0.012 | 0.02 | 2420 | X-RAY DIFFRACTION | r_gen_planes_other0.016 | 0.02 | 512 | X-RAY DIFFRACTION | r_mcbond_it2.336 | 2.941 | 984 | X-RAY DIFFRACTION | r_mcbond_other2.337 | 2.94 | 981 | X-RAY DIFFRACTION | r_mcangle_it3.459 | 4.395 | 1224 | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.25→2.308 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.269 | 47 | - |
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Rwork | 0.246 | 846 | - |
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all | - | 893 | - |
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obs | - | 846 | 99.89 % |
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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 | 0.6233 | 0.9706 | -0.3067 | 4.9556 | 1.5415 | 1.4378 | 0.1236 | -0.0515 | -0.1296 | -0.0308 | -0.1234 | -0.1942 | -0.1041 | -0.0739 | -0.0002 | 0.1642 | -0.0207 | -0.013 | 0.1252 | 0.0382 | 0.2617 | -6.7125 | -4.298 | 29.0018 | 2 | 2.5014 | 0.058 | -0.9783 | 5.4178 | 2.0978 | 1.7206 | -0.0734 | 0.2223 | -0.0359 | -0.0862 | -0.0118 | 0.1495 | -0.1045 | 0.0621 | 0.0852 | 0.0801 | -0.001 | 0.0192 | 0.1226 | 0.0026 | 0.1461 | -4.1369 | 1.6942 | 22.5916 | 3 | 2.0564 | 0.5624 | 0.4526 | 1.0154 | 0.1581 | 0.6106 | 0.023 | -0.0382 | -0.2259 | 0.0979 | -0.0978 | -0.0628 | -0.0578 | 0.2192 | 0.0748 | 0.0921 | 0.0011 | 0.0309 | 0.182 | 0.0315 | 0.1609 | 4.0328 | -0.5393 | 29.4167 | 4 | 1.3489 | -0.9507 | 0.3334 | 2.5835 | -0.1808 | 0.5606 | -0.0138 | -0.0493 | 0.0198 | -0.136 | 0.0759 | 0.0132 | -0.0148 | -0.0955 | -0.0621 | 0.1871 | 0.0197 | 0.0325 | 0.1221 | -0.0071 | 0.0855 | 16.6832 | -12.5878 | 2.6704 | 5 | 19.9764 | -6.9859 | 21.064 | 3.087 | -4.5789 | 34.289 | -0.0601 | -0.3283 | 0.5657 | 0.013 | 0.0421 | -0.3296 | -0.0072 | -0.5625 | 0.018 | 0.252 | -0.1655 | -0.0305 | 0.3686 | 0.063 | 0.1773 | 4.366 | -16.9907 | 6.5874 | 6 | 1.6748 | 0.4335 | -0.4677 | 2.3412 | -1.7719 | 1.75 | -0.0804 | -0.1702 | -0.0752 | -0.0945 | 0.1677 | -0.0952 | -0.0813 | -0.3002 | -0.0874 | 0.1567 | 0.019 | 0.0577 | 0.2239 | 0.0454 | 0.0991 | 16.7686 | -13.6203 | 13.5064 |
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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 | A2 - 32 | 2 | X-RAY DIFFRACTION | 2 | A33 - 58 | 3 | X-RAY DIFFRACTION | 3 | A59 - 124 | 4 | X-RAY DIFFRACTION | 4 | B2 - 60 | 5 | X-RAY DIFFRACTION | 5 | B61 - 67 | 6 | X-RAY DIFFRACTION | 6 | B68 - 124 | | | | | | |
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