ソフトウェア | 名称 | バージョン | 分類 |
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PHASER | | 位相決定 | PHENIX | (phenix.refine: 1.6.4_486)精密化 | XDS | | データ削減 | XDS | | データスケーリング | |
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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 1UT7 + B-DNA model 解像度: 4.113→29.966 Å / SU ML: 0.6 / σ(F): 1.99 / 位相誤差: 36.64 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.349 | 1035 | 10.02 % |
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Rwork | 0.2603 | - | - |
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obs | 0.2688 | 10333 | 99.05 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 159.295 Å2 / ksol: 0.259 e/Å3 |
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原子変位パラメータ | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -32.7247 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 60.8948 Å2 | 0 Å2 |
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3- | - | - | -28.1701 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 4.113→29.966 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4601 | 1066 | 0 | 0 | 5667 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 |
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X-RAY DIFFRACTION | f_bond_d0.015 | 5934 | X-RAY DIFFRACTION | f_angle_d2.484 | 8239 | X-RAY DIFFRACTION | f_dihedral_angle_d23.879 | 2236 | X-RAY DIFFRACTION | f_chiral_restr0.107 | 861 | X-RAY DIFFRACTION | f_plane_restr0.01 | 845 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | タイプ | Rms dev position (Å) |
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1 | 1 | A1078 | X-RAY DIFFRACTION | POSITIONAL | 1 | 2 | C1078 | X-RAY DIFFRACTION | POSITIONAL0.05 | 2 | 1 | B1109 | X-RAY DIFFRACTION | POSITIONAL | 2 | 2 | D1109 | X-RAY DIFFRACTION | POSITIONAL0.034 | | | | | | | | |
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LS精密化 シェル | 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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4.1132-4.3294 | 0.4443 | 139 | 0.3606 | 1250 | X-RAY DIFFRACTION | 95 | 4.3294-4.5998 | 0.351 | 147 | 0.3138 | 1317 | X-RAY DIFFRACTION | 100 | 4.5998-4.9535 | 0.3473 | 146 | 0.2684 | 1313 | X-RAY DIFFRACTION | 100 | 4.9535-5.4493 | 0.3207 | 146 | 0.2476 | 1307 | X-RAY DIFFRACTION | 100 | 5.4493-6.2316 | 0.3704 | 149 | 0.2534 | 1340 | X-RAY DIFFRACTION | 100 | 6.2316-7.828 | 0.3758 | 151 | 0.259 | 1359 | X-RAY DIFFRACTION | 100 | 7.828-29.9667 | 0.3095 | 157 | 0.2267 | 1412 | X-RAY DIFFRACTION | 99 |
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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 | 4.0802 | -6.3141 | -0.4113 | 3.802 | 0.14 | -4.6957 | -0.7356 | 1.9971 | -0.9787 | -0.0258 | 0.2148 | -0.111 | 0.3317 | -0.405 | 0.54 | 1.2752 | -0.4599 | 0.0426 | 1.3267 | -0.2664 | 1.3953 | 20.3066 | -20.3716 | -35.0513 | 2 | -1.3317 | 0.5601 | 1.6524 | 7.6699 | 7.892 | 4.0442 | -0.2296 | -0.9277 | -0.3118 | 2.5972 | 0.5028 | -1.1832 | 2.1878 | -0.5726 | -0.3617 | 2.3264 | 0.1924 | 0.0852 | 1.7264 | 0.6833 | 1.6843 | 25.037 | -18.9177 | -2.2684 | 3 | 5.6899 | -4.1204 | 4.7088 | 0.4297 | -2.425 | -0.4871 | 0.0497 | 0.7135 | 0.0983 | -0.9399 | 0.18 | -0.0949 | -0.528 | 0.1405 | -0.2618 | 1.3372 | -0.0612 | 0.0527 | 1.4672 | 0.1462 | 2.1019 | 14.2695 | 23.8041 | -50.1344 | 4 | 5.2038 | 9.168 | 1.3253 | 9.6201 | -4.6989 | 4.2048 | 0.4462 | -1.2101 | -0.0471 | 2.6308 | -0.7313 | -1.0063 | -1.8409 | -0.5853 | 0.0057 | 2.5258 | 0.2968 | 0.0235 | 1.7699 | -0.149 | 2.0973 | 10.5282 | 20.7519 | -17.5756 | 5 | 6.446 | -1.4865 | 1.2004 | 1.1163 | 2.3089 | 0.971 | -1.458 | 1.0071 | 1.1569 | 0.6604 | -0.2067 | -0.7593 | -2.2251 | -1.7802 | 0.6082 | 4.1745 | -0.1294 | -0.6989 | 1.9594 | 0.2244 | 1.8659 | 17.7057 | 0.2759 | -13.0975 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain A2 | X-RAY DIFFRACTION | 2 | chain B3 | X-RAY DIFFRACTION | 3 | chain C4 | X-RAY DIFFRACTION | 4 | chain D5 | X-RAY DIFFRACTION | 5 | chain E or chain F | | | | |
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