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 | | PHENIX | 1.7.1_743精密化 | | PDB_EXTRACT | 3.11 | データ抽出 | | HKL-2000 | | データ収集 | | HKL-2000 | | データ削減 | | MOLREP | | 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 1VKM 解像度: 2.539→48.069 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.79 / σ(F): 1.37 / 位相誤差: 25.82 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2603 | 1655 | 5.16 % |
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Rwork | 0.1888 | - | - |
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obs | 0.1924 | 32069 | 99.23 % |
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all | - | 32321 | - |
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溶媒の処理 | 減衰半径: 0.95 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 49.924 Å2 / ksol: 0.302 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- | 7.8937 Å2 | 0 Å2 | -0 Å2 |
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2- | - | 0.084 Å2 | 0 Å2 |
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3- | - | - | -7.9777 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.539→48.069 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6406 | 0 | 66 | 207 | 6679 |
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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 | 6593 | X-RAY DIFFRACTION | f_angle_d1.267 | 9014 | X-RAY DIFFRACTION | f_dihedral_angle_d13.985 | 2250 | X-RAY DIFFRACTION | f_chiral_restr0.083 | 1124 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1169 | | | | | |
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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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2.5388-2.6135 | 0.3432 | 133 | 0.2583 | 2433 | X-RAY DIFFRACTION | 97 | 2.6135-2.6979 | 0.3436 | 123 | 0.22 | 2480 | X-RAY DIFFRACTION | 98 | 2.6979-2.7943 | 0.3369 | 154 | 0.228 | 2480 | X-RAY DIFFRACTION | 99 | 2.7943-2.9061 | 0.3176 | 151 | 0.2054 | 2465 | X-RAY DIFFRACTION | 99 | 2.9061-3.0384 | 0.3205 | 159 | 0.2169 | 2456 | X-RAY DIFFRACTION | 99 | 3.0384-3.1986 | 0.2782 | 140 | 0.2021 | 2543 | X-RAY DIFFRACTION | 100 | 3.1986-3.3989 | 0.2792 | 141 | 0.1968 | 2521 | X-RAY DIFFRACTION | 99 | 3.3989-3.6612 | 0.2559 | 132 | 0.1995 | 2535 | X-RAY DIFFRACTION | 100 | 3.6612-4.0295 | 0.2416 | 114 | 0.1694 | 2577 | X-RAY DIFFRACTION | 100 | 4.0295-4.6122 | 0.2069 | 137 | 0.1457 | 2565 | X-RAY DIFFRACTION | 100 | 4.6122-5.8093 | 0.2202 | 132 | 0.1709 | 2618 | X-RAY DIFFRACTION | 100 | 5.8093-48.0772 | 0.2395 | 139 | 0.1941 | 2741 | 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 | 1.0265 | -0.1126 | -0.6134 | 0.5273 | -0.0807 | 0.7707 | -0.0988 | 0.4004 | 0.2261 | -0.2026 | 0.0056 | -0.6549 | -0.261 | 0.6436 | -0.2535 | 0.2443 | -0.3265 | 0.0924 | 0.5326 | -0.0557 | 0.6116 | 31.6206 | -8.4369 | -17.3822 | 2 | 1.358 | -0.3299 | -0.0012 | 0.7869 | -0.9223 | 2.5509 | -0.3016 | 0.2745 | 0.4929 | -0.2692 | 0.0341 | -0.0287 | -0.6259 | 0.2561 | 0.1237 | 0.4817 | -0.2202 | -0.0105 | 0.3123 | 0.0521 | 0.3913 | 18.8909 | -0.4851 | -17.3861 | 3 | 1.3652 | 0.5554 | 1.1041 | 2.8307 | 1.8075 | 1.6079 | -0.2155 | 0.44 | 0.4235 | -0.1893 | 0.0011 | 0.0444 | -0.5375 | -0.0173 | -0.4428 | 0.678 | -0.2845 | 0.1106 | 0.5066 | 0.1819 | 0.39 | 16.1845 | -1.5477 | -27.682 | 4 | 1.1067 | -0.0192 | 0.0565 | 1.3399 | 0.2305 | 1.2269 | -0.1115 | 0.3485 | 0.0371 | -0.2745 | 0.1575 | -0.1018 | -0.2421 | 0.2181 | 0.0258 | 0.1494 | -0.0937 | 0.0043 | 0.2796 | -0.0273 | 0.1926 | 10.0941 | -15.7108 | -19.1481 | 5 | 1.6657 | 0.0381 | 0.0662 | 0.78 | -0.1003 | 1.6448 | -0.1377 | -0.1774 | -0.0775 | -0.0021 | 0.124 | -0.1932 | -0.0761 | 0.1626 | 0.0317 | 0.1015 | -0.0536 | 0.0097 | 0.1431 | -0.0191 | 0.2222 | 12.5312 | -21.299 | -4.7939 | 6 | 2.0527 | 0.1588 | 0.1362 | 0.8324 | 0.2296 | 1.6419 | -0.0375 | 0.2059 | 0.2994 | -0.1363 | 0.0034 | 0.096 | -0.35 | -0.1811 | -0.0155 | 0.1808 | -0.0057 | -0.017 | 0.1917 | 0.0168 | 0.2454 | 5.6636 | -7.2911 | -13.4062 | 7 | 0.477 | 0.357 | 0.5092 | 1.8399 | 0.1815 | 0.5682 | 0.2071 | 0.0799 | -0.7704 | 0.2905 | 0.1677 | -0.1502 | 0.7451 | 0.2025 | -0.126 | 0.6781 | 0.0605 | -0.1267 | 0.222 | -0.0976 | 0.676 | 16.5679 | -49.4887 | -7.3241 | 8 | 0.8737 | 0.1326 | 0.4682 | 1.2959 | 0.347 | 1.2562 | 0.123 | 0.2315 | -0.6774 | 0.0039 | 0.0923 | -0.1552 | 0.696 | 0.0359 | -0.0731 | 0.2779 | -0.1472 | -0.1116 | 0.0183 | -0.2233 | 0.3932 | 8.7677 | -41.2193 | -15.3952 | 9 | 0.1636 | 0.208 | 0.1692 | 1.4911 | 0.1316 | 0.8728 | 0.1543 | 0.2693 | -0.4099 | -0.1724 | 0.182 | 0.1979 | 0.6508 | -0.2158 | 0.1008 | 0.4405 | -0.1964 | -0.1288 | 0.3389 | -0.1741 | 0.4437 | 0.0827 | -46.5229 | -20.2697 | 10 | 0.4048 | -0.2474 | 0.4513 | 0.2456 | -0.1869 | 0.5896 | 0.569 | -0.0495 | 0.098 | -0.0227 | -0.0967 | 0.1831 | 0.4631 | 0.0818 | -0.2522 | 0.759 | 0.0063 | -0.1134 | 0.2418 | -0.1236 | 0.6986 | 9.7354 | -55.5859 | -17.58 | 11 | 0.1431 | -0.2718 | -0.2105 | 1.4719 | -0.5759 | 2.1446 | 0.0302 | 0.183 | -0.1063 | -0.7792 | -0.0309 | -0.2845 | -0.0769 | 0.4118 | -0.0967 | 0.6891 | 0.0107 | 0.1618 | 0.7213 | -0.279 | 0.1291 | 21.6743 | -35.5245 | -51.3449 | 12 | 0.9919 | 0.062 | 0.0885 | 0.9415 | -0.9303 | 0.9479 | 0.0547 | 0.6758 | -0.0529 | -0.4428 | 0.2303 | -0.1622 | 0.3377 | 0.1237 | 0.0023 | 0.8494 | 0.0536 | 0.1442 | 0.8668 | -0.2292 | 0.3887 | 20.4312 | -34.8326 | -55.5552 | 13 | 1.2253 | -0.5863 | -0.4129 | 0.9755 | -0.3663 | 0.6108 | 0.187 | 0.6316 | -0.2742 | -0.7828 | 0.123 | 0.0118 | 0.2936 | 0.1595 | 0.1301 | 0.7442 | -0.108 | 0.0925 | 0.7367 | -0.3226 | 0.2453 | 14.1263 | -38.0186 | -44.909 | 14 | 0.7446 | -0.2637 | 0.0445 | 1.2859 | 0.028 | 0.4292 | 0.0017 | 0.5458 | 0.122 | -0.8437 | 0.237 | 0.0511 | 0.0442 | 0.1141 | -0.1026 | 0.588 | -0.2424 | 0.0022 | 0.594 | -0.0321 | 0.1628 | 7.3609 | -23.4526 | -40.3677 | 15 | 0.4063 | -0.3395 | 0.3472 | 0.9132 | 0.1688 | 0.6209 | 0.2164 | 0.3699 | -0.0155 | -0.8362 | 0.097 | 0.1244 | -0.4977 | 0.2422 | -0.0743 | 0.7782 | -0.2607 | 0.1083 | 0.8068 | 0.004 | 0.0735 | 8.113 | -23.1325 | -49.2345 |
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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 (resseq 5:30)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 31:77)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 78:98)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 99:198)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 199:224)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 225:311)7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resseq 4:57)8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resseq 58:198)9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 199:283)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 284:310)11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resseq 8:42)12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resseq 43:77)13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resseq 78:139)14 | X-RAY DIFFRACTION | 14 | chain 'C' and (resseq 140:198)15 | X-RAY DIFFRACTION | 15 | chain 'C' and (resseq 199:310) | | | | | | | | | | | | | | |
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