ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (1.12_2829)精密化 | HKL-2000 | | データ削減 | HKL-2000 | | 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: 4y1i 解像度: 2.698→46.658 Å / SU ML: 0.43 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 29.03 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2485 | 1916 | 9.99 % |
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Rwork | 0.1958 | - | - |
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obs | 0.2011 | 19173 | 98.71 % |
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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 |
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精密化ステップ | サイクル: LAST / 解像度: 2.698→46.658 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 0 | 4114 | 92 | 45 | 4251 |
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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_d0.002 | 4676 | X-RAY DIFFRACTION | f_angle_d0.513 | 7284 | X-RAY DIFFRACTION | f_dihedral_angle_d13.902 | 2323 | X-RAY DIFFRACTION | f_chiral_restr0.026 | 968 | X-RAY DIFFRACTION | f_plane_restr0.003 | 194 | | | | | |
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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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2.6983-2.7658 | 0.4305 | 126 | 0.3973 | 1132 | X-RAY DIFFRACTION | 91 | 2.7658-2.8405 | 0.4003 | 132 | 0.3575 | 1179 | X-RAY DIFFRACTION | 95 | 2.8405-2.9241 | 0.3624 | 133 | 0.2971 | 1205 | X-RAY DIFFRACTION | 99 | 2.9241-3.0185 | 0.2981 | 136 | 0.2536 | 1223 | X-RAY DIFFRACTION | 99 | 3.0185-3.1263 | 0.2881 | 142 | 0.2353 | 1267 | X-RAY DIFFRACTION | 100 | 3.1263-3.2515 | 0.256 | 136 | 0.2164 | 1242 | X-RAY DIFFRACTION | 100 | 3.2515-3.3994 | 0.2816 | 135 | 0.1976 | 1230 | X-RAY DIFFRACTION | 99 | 3.3994-3.5786 | 0.256 | 137 | 0.1898 | 1232 | X-RAY DIFFRACTION | 100 | 3.5786-3.8027 | 0.2461 | 138 | 0.18 | 1250 | X-RAY DIFFRACTION | 99 | 3.8027-4.0961 | 0.2299 | 137 | 0.1634 | 1228 | X-RAY DIFFRACTION | 100 | 4.0961-4.508 | 0.2051 | 140 | 0.1501 | 1260 | X-RAY DIFFRACTION | 100 | 4.508-5.1596 | 0.1968 | 141 | 0.1554 | 1266 | X-RAY DIFFRACTION | 100 | 5.1596-6.4978 | 0.2031 | 139 | 0.1746 | 1258 | X-RAY DIFFRACTION | 100 | 6.4978-46.6648 | 0.2423 | 144 | 0.1921 | 1285 | 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 | 4.3361 | 0.8662 | 1.5679 | 1.1026 | 1.011 | 0.9966 | -0.0803 | 0.0105 | 0.0912 | -0.1614 | 0.0679 | 0.3246 | -0.0084 | -0.2501 | 0.0565 | 0.3746 | -0.1573 | -0.0038 | 0.7279 | 0.0351 | 0.5122 | 28.7236 | -6.7791 | 21.8418 | 2 | 5.6431 | 2.1439 | -0.0173 | 2.6094 | 0.5207 | 0.0462 | -0.0204 | -0.3425 | 0.104 | -0.1788 | -0.1359 | 0.0157 | -0.0621 | -0.2391 | 0.1355 | 0.3546 | -0.0914 | -0.0058 | 0.5801 | 0.0227 | 0.3749 | 17.668 | -20.6839 | 25.9236 | 3 | 0.5923 | 1.0495 | -0.1078 | 1.8098 | 0.5587 | 4.4793 | -0.231 | 0.0444 | -0.1374 | -0.1979 | -0.0064 | 0.2947 | 0.1259 | -0.1785 | 0.1752 | 0.3021 | -0.012 | 0.0039 | 0.5591 | -0.1167 | 0.5123 | 42.1062 | -0.5811 | 40.4958 | 4 | 7.1112 | 2.0614 | -1.1217 | 2.5583 | 1.3266 | 5.449 | -0.17 | -0.4152 | -0.2432 | -0.1395 | -0.1825 | 0.1061 | -0.0988 | -0.4067 | 0.3071 | 0.5935 | -0.0281 | -0.2897 | 0.4811 | 0.1075 | 0.7519 | 6.5979 | -4.9112 | 7.0502 | 5 | 4.8883 | 2.9314 | -3.8437 | 2.0899 | -2.1159 | 5.2424 | -0.426 | 0.245 | -0.554 | -0.5664 | 0.0517 | 0.2232 | 0.4286 | -0.0335 | 0.4262 | 0.5731 | -0.0168 | 0.1244 | 0.8292 | -0.0549 | 0.6627 | 38.5434 | -26.8393 | 7.4112 | 6 | 3.8654 | -0.2157 | -1.1586 | 5.3849 | -1.3494 | 5.9042 | 0.1044 | -0.425 | -0.2458 | -0.2415 | -0.4184 | -0.1354 | 0.5455 | 0.4317 | 0.3266 | 0.4324 | -0.0746 | 0.0877 | 0.7084 | -0.0185 | 0.4132 | 55.914 | -15.6863 | 13.4515 | 7 | 5.8601 | -1.71 | 4.5321 | 1.9984 | -3.281 | 7.379 | 1.5317 | -0.6332 | -0.7364 | 3.0687 | 0.8778 | -0.5492 | 1.0558 | -0.0008 | -2.0196 | 4.9274 | 0.2003 | 0.1718 | 1.3996 | 0.2371 | 2.644 | 57.1034 | -43.28 | 27.5869 | 8 | 5.4016 | -0.1281 | -0.2342 | 5.3671 | 0.0633 | 2.5375 | -0.6302 | 0.5277 | -0.2006 | -1.3325 | 0.0606 | 0.4494 | 0.2718 | -0.0698 | 0.6152 | 0.8918 | -0.077 | 0.0347 | 0.9223 | -0.2388 | 0.6424 | 45.3134 | -23.3017 | -4.1872 |
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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 3:35)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 36:71)3 | X-RAY DIFFRACTION | 3 | (chain A and resid 72:91)4 | X-RAY DIFFRACTION | 4 | (chain A and resid 92:102)5 | X-RAY DIFFRACTION | 5 | (chain B and resid 3:28)6 | X-RAY DIFFRACTION | 6 | (chain B and resid 29:74)7 | X-RAY DIFFRACTION | 7 | (chain B and resid 82:85)8 | X-RAY DIFFRACTION | 8 | (chain B and resid 86:101) | | | | | | | |
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