ソフトウェア | 名称 | バージョン | 分類 |
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Blu-Ice | | データ収集 | PHENIX | | モデル構築 | PHENIX | (phenix.refine: 1.8.1_1168)精密化 | XDS | | データ削減 | SCALA | | 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: フーリエ合成 / 解像度: 1.7→19.523 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8858 / SU ML: 0.16 / σ(F): 1.97 / 位相誤差: 18.81 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.1796 | 1530 | 1.69 % | RANDOM |
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Rwork | 0.1528 | - | - | - |
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all | 0.1533 | 99532 | - | - |
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obs | 0.1533 | 90551 | 91.37 % | - |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso max: 154.33 Å2 / Biso mean: 20.8356 Å2 / Biso min: 3.61 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 1.7→19.523 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 7172 | 0 | 117 | 1132 | 8421 |
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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_d0.006 | 7533 | X-RAY DIFFRACTION | f_angle_d1.058 | 10264 | X-RAY DIFFRACTION | f_dihedral_angle_d14.313 | 2707 | X-RAY DIFFRACTION | f_chiral_restr0.071 | 1147 | X-RAY DIFFRACTION | f_plane_restr0.004 | 1340 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | % reflection obs (%) |
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1.7-1.7548 | 0.2529 | 124 | 0.1904 | 7338 | 83 | 1.7548-1.8175 | 0.2185 | 130 | 0.1851 | 7497 | 85 | 1.8175-1.8902 | 0.2479 | 126 | 0.1754 | 7609 | 86 | 1.8902-1.9762 | 0.2022 | 136 | 0.1723 | 7855 | 89 | 1.9762-2.0803 | 0.1976 | 137 | 0.1583 | 7958 | 90 | 2.0803-2.2104 | 0.2092 | 137 | 0.152 | 8120 | 92 | 2.2104-2.3808 | 0.1411 | 140 | 0.1542 | 8309 | 94 | 2.3808-2.6199 | 0.1909 | 144 | 0.155 | 8443 | 95 | 2.6199-2.9978 | 0.2296 | 148 | 0.16 | 8525 | 96 | 2.9978-3.7725 | 0.161 | 152 | 0.1426 | 8665 | 98 | 3.7725-19.5241 | 0.1341 | 156 | 0.1346 | 8702 | 98 |
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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 | 0.7483 | -0.1334 | -0.0664 | 1.136 | -0.1491 | 2.0623 | 0.0108 | -0.0641 | 0.0763 | 0.087 | 0.0151 | 0.0424 | -0.3954 | 0.0771 | 0.0018 | 0.3165 | -0.0104 | -0.0148 | 0.1065 | -0.007 | 0.098 | 27.3614 | 114.8073 | 88.16 | 2 | 0.7494 | 0.0097 | 0.6951 | 0.8362 | 0.0307 | 3.0143 | -0.0431 | -0.029 | 0.0902 | 0.0825 | -0.0037 | 0.0405 | -0.3161 | -0.1212 | 0.0444 | 0.209 | 0.0121 | -0.009 | 0.0819 | 0.0026 | 0.0813 | 24.6439 | 106.2992 | 84.8485 | 3 | 0.2958 | 0.4038 | 0.2969 | 1.9281 | 0.9308 | 1.5814 | 0.0021 | 0.0304 | 0.0369 | -0.026 | 0.0008 | -0.0198 | -0.1161 | 0.1485 | 0.0004 | 0.1324 | 0.0126 | -0.0005 | 0.1279 | 0.0079 | 0.0527 | 29.9078 | 98.7381 | 74.0715 | 4 | 7.0461 | 3.6049 | 4.1019 | 3.6852 | -0.3758 | 5.7136 | -0.1339 | -1.0319 | 0.8455 | 0.3667 | -0.1474 | 0.0039 | -0.6308 | -0.1984 | 0.2136 | 0.7756 | 0.0338 | 0.022 | 1.0871 | -0.3 | 1.3061 | 3.8068 | 104.1674 | 76.2288 | 5 | 1.0575 | 0.8558 | 0.1324 | 1.761 | 0.2641 | 2.3428 | -0.2267 | -0.3186 | 0.1843 | 0.1694 | 0.0947 | 0.0309 | 0.0482 | -0.1098 | 0.0799 | 0.199 | 0.0653 | 0.0028 | 0.1434 | -0.0417 | 0.0653 | 22.5935 | 80.2204 | 62.3439 | 6 | 0.4874 | 0.1727 | 0.0613 | 1.0025 | 0.2543 | 1.312 | 0.0138 | -0.0059 | 0.0201 | 0.0848 | 0.018 | -0.0086 | 0.2567 | 0.0294 | -0.0115 | 0.1983 | 0.0152 | -0.011 | 0.1063 | -0.0065 | 0.0569 | 23.3945 | 84.923 | 71.8328 | 7 | 4.1776 | -0.1291 | -1.0659 | 3.264 | -1.3303 | 6.2783 | -0.0564 | -0.4029 | 0.0593 | 0.3238 | 0.0211 | -0.2939 | -0.1017 | 0.5301 | 0.1002 | 0.2593 | 0.0321 | -0.0723 | 0.1554 | 0.0032 | 0.1141 | 34.1997 | 92.4264 | 93.4088 |
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精密化 TLSグループ | ID | Refine-ID | Refine TLS-ID | Selection details | Auth asym-ID | Auth seq-ID |
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1 | X-RAY DIFFRACTION | 1 | (chain A and resid 1:51)A1 - 51 | 2 | X-RAY DIFFRACTION | 2 | (chain A and resid 52:127)A52 - 127 | 3 | X-RAY DIFFRACTION | 3 | (chain A and resid 128:229)A128 - 229 | 4 | X-RAY DIFFRACTION | 4 | (chain A and resid 230:242)A230 - 242 | 5 | X-RAY DIFFRACTION | 5 | (chain A and resid 243:282)A243 - 282 | 6 | X-RAY DIFFRACTION | 6 | (chain A and resid 283:461)A283 - 461 | 7 | X-RAY DIFFRACTION | 7 | (chain A and resid 462:469)A462 - 469 | | | | | | | | | | | | | | |
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