ソフトウェア | 名称 | バージョン | 分類 | NB |
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SCALA | 3.3.9data processing | PHENIX | 1.6.4_486精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | ADSC | Quantumデータ収集 | | MOSFLM | | データ削減 | | SCALA | | データスケーリング | | PHASER | | 位相決定 | | | | | |
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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 3PPC 解像度: 2.8→47.664 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.48 / σ(F): 1.35 / 位相誤差: 28.88 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2756 | 2028 | 4.25 % |
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Rwork | 0.2103 | - | - |
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obs | 0.2132 | 47729 | 99.72 % |
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all | - | 47736 | - |
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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: 35.532 Å2 / ksol: 0.285 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- | 5.0267 Å2 | 0 Å2 | 6.934 Å2 |
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2- | - | -5.0978 Å2 | 0 Å2 |
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3- | - | - | 0.0711 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.8→47.664 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 10989 | 0 | 0 | 51 | 11040 |
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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_d0.008 | 11223 | X-RAY DIFFRACTION | f_angle_d1.153 | 15343 | X-RAY DIFFRACTION | f_dihedral_angle_d14.095 | 3846 | X-RAY DIFFRACTION | f_chiral_restr0.072 | 1800 | X-RAY DIFFRACTION | f_plane_restr0.005 | 2010 | | | | | |
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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 | A5290 | X-RAY DIFFRACTION | POSITIONAL | 1 | 2 | B5290 | X-RAY DIFFRACTION | POSITIONAL0.056 | | | | |
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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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2.8-2.8701 | 0.4438 | 144 | 0.3637 | 3222 | X-RAY DIFFRACTION | 100 | 2.8701-2.9476 | 0.3774 | 131 | 0.3066 | 3233 | X-RAY DIFFRACTION | 100 | 2.9476-3.0344 | 0.3535 | 165 | 0.2789 | 3221 | X-RAY DIFFRACTION | 100 | 3.0344-3.1323 | 0.3364 | 137 | 0.2477 | 3264 | X-RAY DIFFRACTION | 100 | 3.1323-3.2442 | 0.3293 | 144 | 0.2415 | 3257 | X-RAY DIFFRACTION | 100 | 3.2442-3.3741 | 0.3383 | 144 | 0.2409 | 3273 | X-RAY DIFFRACTION | 100 | 3.3741-3.5276 | 0.3077 | 142 | 0.2448 | 3271 | X-RAY DIFFRACTION | 100 | 3.5276-3.7135 | 0.3033 | 138 | 0.2179 | 3247 | X-RAY DIFFRACTION | 100 | 3.7135-3.9461 | 0.2697 | 148 | 0.196 | 3275 | X-RAY DIFFRACTION | 100 | 3.9461-4.2506 | 0.2627 | 146 | 0.1757 | 3252 | X-RAY DIFFRACTION | 100 | 4.2506-4.678 | 0.2064 | 149 | 0.1543 | 3283 | X-RAY DIFFRACTION | 100 | 4.678-5.3541 | 0.2104 | 159 | 0.1664 | 3266 | X-RAY DIFFRACTION | 100 | 5.3541-6.7426 | 0.2751 | 134 | 0.2116 | 3268 | X-RAY DIFFRACTION | 98 | 6.7426-47.6706 | 0.2319 | 147 | 0.1935 | 3369 | X-RAY DIFFRACTION | 100 |
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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 | 0.078 | 0.0795 | 0.0708 | 0.7954 | 0.1969 | 0.3772 | -0.107 | 0.0626 | 0.1496 | -0.0919 | 0.231 | 0.5801 | -0.2472 | 0.0187 | -0.1313 | 0.3154 | -0.1097 | 0.1102 | 0.1193 | 0.0431 | 0.2643 | -22.0797 | -8.5558 | 51.1089 | 2 | 0.7502 | 0.1611 | 0.5449 | 1.1459 | 0.0117 | 0.6344 | -0.1197 | 0.074 | 0.0409 | 0.025 | 0.0912 | 0.2692 | -0.3159 | 0.1766 | 0.0717 | 0.2537 | -0.0835 | -0.0899 | 0.109 | -0.0284 | 0.2375 | -18.6702 | -5.8854 | 35.8124 | 3 | 1.0757 | 0.4172 | -0.4345 | 1.3455 | -0.1188 | 0.3833 | 0.1335 | -0.3212 | 0.4007 | 0.3877 | 0.119 | 0.3378 | -0.2265 | 0.0661 | -0.1921 | 0.2782 | -0.0694 | 0.0841 | 0.1051 | -0.0067 | 0.1009 | -10.5212 | 5.5564 | 56.5417 | 4 | 1.2686 | 0.1896 | -1.1081 | 0.0946 | -0.3102 | 1.2461 | -0.5885 | -0.0937 | -0.6636 | -0.063 | 0.0483 | -0.1053 | 0.6478 | 0.1309 | 0.5303 | 0.535 | 0.0172 | 0.3542 | 0.0713 | 0.067 | 0.3327 | 12.8154 | -25.9872 | 39.6906 | 5 | 1.3959 | 0.8924 | -1.2485 | 0.6493 | -0.8978 | 1.4354 | -0.3017 | -0.1098 | -0.4946 | -0.0482 | -0.1598 | -0.2766 | 0.3787 | 0.0648 | 0.358 | 0.2366 | -0.0661 | 0.1452 | 0.0593 | -0.028 | 0.1555 | 10.9104 | -16.7687 | 45.5228 | 6 | 0.0698 | 0.0641 | -0.0751 | 0.4668 | -0.0331 | 0.2654 | -0.1074 | 0.0287 | -0.025 | 0.1018 | -0.0739 | -0.0548 | 0.2146 | -0.1762 | 0.1023 | 0.3226 | -0.1463 | 0.1249 | 0.1364 | -0.1166 | 0.1333 | 8.4299 | -16.105 | 22.1153 | 7 | 0.3788 | -0.1672 | 0.3595 | 0.5173 | -0.1855 | 0.3662 | -0.0724 | -0.0998 | 0.0238 | -0.1694 | 0.0594 | 0.2096 | -0.0387 | -0.1028 | -0.0058 | 0.0742 | 0.035 | -0.0566 | 0.0748 | -0.0183 | 0.2091 | -54.9518 | -35.8607 | -5.7511 | 8 | 0.0342 | 0.0586 | -0.0991 | 0.4211 | -0.3529 | 0.4391 | -0.1459 | -0.0753 | -0.0204 | -0.3438 | -0.0107 | -0.0916 | 0.384 | 0.1271 | -0.1791 | -0.0364 | 0.0629 | -0.1106 | 0.0608 | -0.0097 | 0.0516 | -46.7944 | -49.6185 | 2.0187 | 9 | 0.9283 | 0.2963 | -0.9912 | 0.2173 | -0.1257 | 1.4978 | 0.4621 | -0.0768 | 0.4648 | 0.3899 | -0.0212 | 0.2349 | -0.6124 | 0.173 | -0.4179 | 0.6288 | -0.1033 | 0.3731 | 0.1098 | -0.0367 | 0.2766 | -58.2303 | -18.0626 | 28.8471 | 10 | 0.785 | 0.6753 | -0.4918 | 1.249 | -0.9875 | 0.8276 | 0.3112 | -0.0968 | 0.2086 | 0.4448 | -0.1438 | 0.3662 | -0.3573 | 0.2022 | -0.1205 | 0.1787 | -0.0999 | 0.0819 | 0.0888 | -0.0097 | 0.1407 | -52.1802 | -28.0497 | 26.0662 | 11 | 0.2945 | -0.0458 | -0.0855 | 0.1065 | 0.0514 | 0.1283 | -0.2967 | 0.031 | -0.3316 | 0.3571 | 0.0672 | 0.1619 | 0.1674 | 0.0072 | 0.2048 | 0.3772 | 0.0369 | 0.2372 | 0.1129 | -0.0641 | 0.2754 | -74.2282 | -31.6212 | 28.1205 | 12 | 0.2933 | -0.1708 | -0.1293 | 0.2872 | -0.2347 | 0.5771 | 0.1417 | 0.0607 | 0.0359 | -0.0133 | 0.0388 | 0.2559 | -0.1567 | -0.0824 | -0.1843 | 0.4024 | 0.1987 | 0.4796 | 0.239 | 0.2326 | 0.5769 | -77.898 | -17.3717 | 23.0402 |
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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 A and resid 1:101)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 102:144)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 145:395)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 396:505)5 | X-RAY DIFFRACTION | 5 | (chain A and resid 506:660)6 | X-RAY DIFFRACTION | 6 | (chain A and resid 663:766)7 | X-RAY DIFFRACTION | 7 | (chain B and resid 1:137)8 | X-RAY DIFFRACTION | 8 | (chain B and resid 138:399)9 | X-RAY DIFFRACTION | 9 | (chain B and resid 400:507)10 | X-RAY DIFFRACTION | 10 | (chain B and resid 508:655)11 | X-RAY DIFFRACTION | 11 | (chain B and resid 656:735)12 | X-RAY DIFFRACTION | 12 | (chain B and resid 736:767) | | | | | | | | | | | |
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