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 | SOLVE | | 位相決定 | PHENIX | (phenix.refine: 1.7.1_743)精密化 | HKL-2000 | | データ削減 | HKL-2000 | | データスケーリング | |
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精密化 | 構造決定の手法: 多重同系置換 / 解像度: 2.4→45.703 Å / SU ML: 0.69 / σ(F): 0 / 位相誤差: 25.93 / 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 | 0.251 | 2261 | 5.06 % | RANDOM |
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Rwork | 0.1948 | - | - | - |
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all | 0.1976 | 46944 | - | - |
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obs | 0.1976 | 44683 | 98.73 % | - |
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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: 64.819 Å2 / ksol: 0.354 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- | -2.1382 Å2 | -0 Å2 | 0.9995 Å2 |
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2- | - | -0.424 Å2 | -0 Å2 |
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3- | - | - | 5.1407 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.4→45.703 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 7514 | 0 | 0 | 321 | 7835 |
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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 | 7699 | X-RAY DIFFRACTION | f_angle_d1.094 | 10452 | X-RAY DIFFRACTION | f_dihedral_angle_d15.354 | 2912 | X-RAY DIFFRACTION | f_chiral_restr0.073 | 1128 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1380 | | | | | |
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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 | A3757 | X-RAY DIFFRACTION | POSITIONAL0.046 | 1 | 2 | B3757 | X-RAY DIFFRACTION | POSITIONAL0.046 | | | | |
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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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2.4-2.4522 | 0.3364 | 127 | 0.2612 | 2594 | X-RAY DIFFRACTION | 98 | 2.4522-2.5092 | 0.3561 | 150 | 0.2585 | 2588 | X-RAY DIFFRACTION | 98 | 2.5092-2.572 | 0.3007 | 138 | 0.2558 | 2609 | X-RAY DIFFRACTION | 98 | 2.572-2.6415 | 0.3501 | 146 | 0.2504 | 2584 | X-RAY DIFFRACTION | 98 | 2.6415-2.7192 | 0.3229 | 142 | 0.2557 | 2607 | X-RAY DIFFRACTION | 98 | 2.7192-2.807 | 0.3384 | 134 | 0.2366 | 2672 | X-RAY DIFFRACTION | 99 | 2.807-2.9073 | 0.2793 | 139 | 0.2136 | 2601 | X-RAY DIFFRACTION | 99 | 2.9073-3.0237 | 0.2677 | 123 | 0.2155 | 2702 | X-RAY DIFFRACTION | 99 | 3.0237-3.1612 | 0.298 | 143 | 0.2132 | 2644 | X-RAY DIFFRACTION | 100 | 3.1612-3.3279 | 0.3386 | 144 | 0.2147 | 2675 | X-RAY DIFFRACTION | 100 | 3.3279-3.5363 | 0.2447 | 148 | 0.2071 | 2671 | X-RAY DIFFRACTION | 100 | 3.5363-3.8092 | 0.2545 | 141 | 0.1805 | 2693 | X-RAY DIFFRACTION | 100 | 3.8092-4.1923 | 0.2504 | 143 | 0.17 | 2699 | X-RAY DIFFRACTION | 100 | 4.1923-4.7984 | 0.21 | 141 | 0.1551 | 2713 | X-RAY DIFFRACTION | 100 | 4.7984-6.0433 | 0.1916 | 145 | 0.1724 | 2717 | X-RAY DIFFRACTION | 100 | 6.0433-45.7111 | 0.2088 | 157 | 0.19 | 2653 | X-RAY DIFFRACTION | 94 |
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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 | 2.8022 | 0.0818 | -1.1062 | 2.176 | 0.3497 | 3.7567 | 0.0764 | 0.0554 | -0.137 | -0.1628 | -0.1537 | 0.4091 | -0.0665 | -0.3746 | 0.0603 | 0.1825 | 0.0289 | -0.062 | 0.2532 | -0.0109 | 0.3548 | 59.6015 | 24.0566 | 59.154 | 2 | 4.7554 | -4.0919 | 0.5948 | 7.7064 | -0.0231 | 3.0219 | 0.2886 | 0.2021 | -0.0926 | -0.6157 | 0.0008 | -0.5572 | 0.26 | 0.1549 | -0.2527 | 0.2999 | -0.0355 | 0.0338 | 0.4099 | -0.1304 | 0.3273 | 88.6825 | 4.4773 | 44.3981 | 3 | 4.2981 | 0.7117 | -0.7262 | 2.6153 | -0.6565 | 2.8077 | 0.1532 | -0.2081 | 0.0012 | 0.4955 | -0.1153 | -0.0266 | -0.4349 | -0.0617 | -0.0292 | 0.5739 | 0.0153 | -0.019 | 0.334 | 0.0148 | 0.2048 | 39.9455 | 50.8727 | 25.2472 | 4 | 3.1298 | 1.5737 | -0.7907 | 6.1861 | -2.4424 | 3.7269 | -0.1488 | -0.3021 | -0.0077 | -0.0098 | -0.0239 | -0.658 | -0.5699 | 0.1733 | 0.1692 | 0.5462 | -0.1194 | -0.0432 | 0.5916 | -0.0544 | 0.3646 | 65.9879 | 70.4022 | 5.5459 |
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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 5:367)2 | X-RAY DIFFRACTION | 2 | (chain A and resid 368:496)3 | X-RAY DIFFRACTION | 3 | (chain B and resid 5:367)4 | X-RAY DIFFRACTION | 4 | (chain B and resid 368:496) | | | |
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