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 | | REFMAC | 5.5.0109精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | SBC-Collect | | データ収集 | | HKL-3000 | | データ削減 | | HKL-3000 | | データスケーリング | | PHENIX | | 位相決定 | | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.14→37.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 13.89 / SU ML: 0.16 / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 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. U VALUES: WITH TLS ADDED
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2478 | 2332 | 5 % | RANDOM |
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Rwork | 0.1962 | - | - | - |
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all | 0.1988 | 46743 | - | - |
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obs | 0.1988 | 46743 | 99.08 % | - |
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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 max: 133.61 Å2 / Biso mean: 44.7822 Å2 / Biso min: 13.93 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.83 Å2 | 0 Å2 | 0.66 Å2 |
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2- | - | 4.27 Å2 | 0 Å2 |
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3- | - | - | -2.16 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.14→37.28 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5652 | 0 | 50 | 173 | 5875 |
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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_d0.018 | 0.022 | 5886 | X-RAY DIFFRACTION | r_bond_other_d0.001 | 0.02 | 3852 | X-RAY DIFFRACTION | r_angle_refined_deg1.59 | 1.954 | 7977 | X-RAY DIFFRACTION | r_angle_other_deg0.873 | 3 | 9492 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg6.509 | 5 | 724 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg43.229 | 25.541 | 296 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg16.146 | 15 | 1070 | X-RAY DIFFRACTION | r_dihedral_angle_4_deg15.676 | 15 | 17 | X-RAY DIFFRACTION | r_chiral_restr0.093 | 0.2 | 901 | X-RAY DIFFRACTION | r_gen_planes_refined0.006 | 0.02 | 6485 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 1128 | X-RAY DIFFRACTION | r_mcbond_it0.862 | 1.5 | 3536 | X-RAY DIFFRACTION | r_mcbond_other0.199 | 1.5 | 1432 | X-RAY DIFFRACTION | r_mcangle_it1.658 | 2 | 5756 | X-RAY DIFFRACTION | r_scbond_it2.754 | 3 | 2350 | X-RAY DIFFRACTION | r_scangle_it4.609 | 4.5 | 2209 | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.139→2.195 Å / Total num. of bins used: 20
| Rfactor | 反射数 | %反射 |
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Rfree | 0.337 | 139 | - |
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Rwork | 0.284 | 3030 | - |
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all | - | 3169 | - |
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obs | - | 3469 | 91.59 % |
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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 | 2.3418 | -0.2861 | 0.2893 | 0.8266 | -0.4512 | 0.4267 | -0.039 | -0.1408 | 0.0747 | -0.006 | 0.0027 | 0.0492 | 0.0567 | -0.01 | 0.0363 | 0.0258 | 0.0204 | 0.0152 | 0.0562 | -0.0085 | 0.0284 | 30.8493 | 49.6478 | 47.8789 | 2 | 1.1341 | 0.6238 | -0.235 | 1.3444 | -0.0384 | 0.5989 | -0.0256 | 0.1966 | -0.0393 | -0.0901 | 0.0861 | -0.0652 | -0.0157 | -0.1098 | -0.0605 | 0.0208 | 0.0075 | 0.0001 | 0.0485 | -0.0047 | 0.0367 | 50.6762 | 38.9243 | 34.3024 | 3 | 1.5296 | -1.4682 | -0.1988 | 1.6089 | -0.0142 | 0.7878 | -0.0086 | -0.0442 | 0.0881 | 0.0948 | 0.0401 | -0.0596 | -0.0134 | -0.159 | -0.0315 | 0.0711 | -0.0393 | 0.0111 | 0.0702 | 0.0083 | 0.0309 | 74.841 | 38.3752 | 12.9608 | 4 | 3.3425 | -0.8102 | -0.1257 | 0.907 | 0.0196 | 4.0452 | 0.0145 | -0.2463 | 0.6278 | 0.0602 | -0.0086 | -0.0937 | -0.6586 | 0.4746 | -0.0058 | 0.1458 | -0.0734 | 0.0267 | 0.1364 | 0.0012 | 0.1728 | 90.1311 | 49.1987 | -5.7546 |
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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 - 175 | 2 | X-RAY DIFFRACTION | 1 | A193 - 239 | 3 | X-RAY DIFFRACTION | 2 | B0 - 174 | 4 | X-RAY DIFFRACTION | 2 | B193 - 251 | 5 | X-RAY DIFFRACTION | 3 | C0 - 176 | 6 | X-RAY DIFFRACTION | 3 | C193 - 232 | 7 | X-RAY DIFFRACTION | 4 | D-1 - 174 | 8 | X-RAY DIFFRACTION | 4 | D193 - 219 | | | | | | | | |
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