ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.20_4459精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | HKL2Map | | 位相決定 | |
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精密化 | 構造決定の手法: 単波長異常分散 / 解像度: 2.33→47.33 Å / SU ML: 0.4152 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 35.3302 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2718 | 7086 | 5 % |
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Rwork | 0.2294 | 134609 | - |
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obs | 0.2315 | 141695 | 99.91 % |
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL |
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原子変位パラメータ | Biso mean: 78.67 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.33→47.33 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 19955 | 0 | 6 | 62 | 20023 |
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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_d0.0023 | 20240 | X-RAY DIFFRACTION | f_angle_d0.5269 | 27430 | X-RAY DIFFRACTION | f_chiral_restr0.0336 | 3236 | X-RAY DIFFRACTION | f_plane_restr0.0042 | 3589 | X-RAY DIFFRACTION | f_dihedral_angle_d14.764 | 7475 | | | | | |
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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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2.33-2.36 | 0.48 | 229 | 0.4252 | 4361 | X-RAY DIFFRACTION | 98.86 | 2.36-2.38 | 0.4586 | 236 | 0.4052 | 4484 | X-RAY DIFFRACTION | 99.96 | 2.38-2.41 | 0.4364 | 233 | 0.3871 | 4441 | X-RAY DIFFRACTION | 99.91 | 2.41-2.44 | 0.4116 | 235 | 0.381 | 4459 | X-RAY DIFFRACTION | 99.94 | 2.44-2.48 | 0.416 | 233 | 0.3669 | 4420 | X-RAY DIFFRACTION | 99.94 | 2.48-2.51 | 0.4246 | 233 | 0.3594 | 4416 | X-RAY DIFFRACTION | 99.89 | 2.51-2.55 | 0.3735 | 234 | 0.3467 | 4460 | X-RAY DIFFRACTION | 99.98 | 2.55-2.58 | 0.3507 | 236 | 0.3277 | 4475 | X-RAY DIFFRACTION | 99.98 | 2.58-2.62 | 0.3657 | 233 | 0.3244 | 4420 | X-RAY DIFFRACTION | 99.96 | 2.62-2.67 | 0.3986 | 234 | 0.3078 | 4457 | X-RAY DIFFRACTION | 99.96 | 2.67-2.71 | 0.3201 | 236 | 0.3039 | 4475 | X-RAY DIFFRACTION | 99.96 | 2.71-2.76 | 0.3706 | 234 | 0.3074 | 4446 | X-RAY DIFFRACTION | 99.79 | 2.76-2.82 | 0.4029 | 234 | 0.325 | 4456 | X-RAY DIFFRACTION | 99.89 | 2.82-2.87 | 0.3478 | 234 | 0.3169 | 4446 | X-RAY DIFFRACTION | 99.96 | 2.87-2.94 | 0.3789 | 234 | 0.3084 | 4447 | X-RAY DIFFRACTION | 99.91 | 2.94-3 | 0.3299 | 237 | 0.2947 | 4501 | X-RAY DIFFRACTION | 99.96 | 3-3.08 | 0.3764 | 235 | 0.2876 | 4455 | X-RAY DIFFRACTION | 99.98 | 3.08-3.16 | 0.3636 | 235 | 0.2804 | 4476 | X-RAY DIFFRACTION | 99.98 | 3.16-3.26 | 0.3343 | 236 | 0.2798 | 4473 | X-RAY DIFFRACTION | 99.96 | 3.26-3.36 | 0.3252 | 236 | 0.2689 | 4493 | X-RAY DIFFRACTION | 99.96 | 3.36-3.48 | 0.2978 | 235 | 0.26 | 4465 | X-RAY DIFFRACTION | 99.94 | 3.48-3.62 | 0.291 | 237 | 0.2398 | 4496 | X-RAY DIFFRACTION | 99.98 | 3.62-3.78 | 0.2539 | 237 | 0.2155 | 4507 | X-RAY DIFFRACTION | 99.96 | 3.78-3.98 | 0.2373 | 237 | 0.2022 | 4496 | X-RAY DIFFRACTION | 99.96 | 3.98-4.23 | 0.2132 | 239 | 0.1915 | 4546 | X-RAY DIFFRACTION | 100 | 4.23-4.56 | 0.2214 | 238 | 0.174 | 4510 | X-RAY DIFFRACTION | 100 | 4.56-5.02 | 0.2217 | 240 | 0.1741 | 4563 | X-RAY DIFFRACTION | 100 | 5.02-5.74 | 0.2529 | 240 | 0.1908 | 4556 | X-RAY DIFFRACTION | 100 | 5.74-7.23 | 0.2232 | 243 | 0.1992 | 4626 | X-RAY DIFFRACTION | 99.98 | 7.23-47.33 | 0.1824 | 253 | 0.1593 | 4783 | X-RAY DIFFRACTION | 99.72 |
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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 | 0.6681035611 | 0.298035742748 | -0.21468828577 | 0.612792014339 | -0.0922541493231 | 0.594099802025 | -0.0451000553487 | 0.209881296065 | -0.18332482329 | -0.0609866021821 | 0.0267732912519 | -0.0210003931869 | 0.00468459656872 | -0.137304079548 | 0.0210336776055 | 0.421659540343 | 0.0244502528617 | -0.00657123281158 | 0.78857164853 | 0.026966147942 | 0.521552458787 | 25.3303427685 | 54.781047275 | 55.3200315853 | 2 | 1.33447787004 | -0.165882696613 | -0.202834797161 | 0.13683692583 | -0.0818136905283 | -0.0890196709383 | 0.161038362713 | 0.337385057704 | -0.225587330905 | -0.0916185916802 | -0.106291331449 | -0.0607293558558 | -0.0309013401073 | 0.0298674679901 | -0.0505415908753 | 0.604694092887 | 0.115110784672 | -0.0269885087368 | 0.765347644473 | 0.0238191434246 | 0.51160412691 | 69.1891516506 | 73.8591880892 | 18.528855508 | 3 | 1.20270591669 | 0.262099779981 | 0.0135481065782 | 0.773162186795 | -0.026721642902 | 0.889972623427 | -0.0305617399194 | -0.0270500222739 | -0.138543480903 | 0.0344290878824 | 0.136203247802 | -0.101760951335 | 0.0906328194394 | 0.228931728492 | -0.0862232101878 | 0.386218726967 | 0.0690266494378 | -0.0147265405407 | 0.751308177644 | 0.0487276210182 | 0.583682654398 | 75.131734361 | 50.6355422637 | 69.7378547833 |
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精密化 TLSグループ | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A ID | Refine TLS-ID | Selection details | Auth seq-ID | Label seq-ID |
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1 | 1 | chain 'A' and (resid 7 through 1381 )7 - 1381 | 1 - 1375 | 2 | 2 | chain 'A' and (resid 1382 through 2064 )1382 - 2064 | 1376 - 2058 | 3 | 3 | chain 'A' and (resid 2065 through 2639 )2065 - 2639 | 2059 - 2633 | | | |
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