ソフトウェア | 名称 | バージョン | 分類 |
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BUSTER | 2.10.4 (24-FEB-2021) | 精密化 | HKL-2000 | | データ削減 | HKL-2000 | | 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: 分子置換 開始モデル: 6OMI 解像度: 2.35→25.24 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.432 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.419 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.263
| Rfactor | 反射数 | %反射 | Selection details |
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Rfree | 0.2566 | 1998 | 6.63 % | RANDOM |
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Rwork | 0.2095 | - | - | - |
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obs | 0.2126 | 30117 | 98.4 % | - |
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原子変位パラメータ | Biso mean: 74.88 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -1.9453 Å2 | 0 Å2 | 0 Å2 |
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2- | - | 18.0131 Å2 | 0 Å2 |
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3- | - | - | -16.0679 Å2 |
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Refine analyze | Luzzati coordinate error obs: 0.33 Å |
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精密化ステップ | サイクル: LAST / 解像度: 2.35→25.24 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 5588 | 0 | 72 | 16 | 5676 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | 数 | Restraint function | Weight |
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X-RAY DIFFRACTION | t_bond_d0.009 | 5802 | HARMONIC2 | X-RAY DIFFRACTION | t_angle_deg1.03 | 7890 | HARMONIC2 | X-RAY DIFFRACTION | t_dihedral_angle_d | 1945 | SINUSOIDAL2 | X-RAY DIFFRACTION | t_incorr_chiral_ct | | | | X-RAY DIFFRACTION | t_pseud_angle | | | | X-RAY DIFFRACTION | t_trig_c_planes | | | | X-RAY DIFFRACTION | t_gen_planes | 972 | HARMONIC5 | X-RAY DIFFRACTION | t_it | 5802 | HARMONIC10 | X-RAY DIFFRACTION | t_nbd | | | | X-RAY DIFFRACTION | t_omega_torsion3.16 | | | | X-RAY DIFFRACTION | t_other_torsion20.19 | | | | X-RAY DIFFRACTION | t_improper_torsion | | | | X-RAY DIFFRACTION | t_chiral_improper_torsion | 751 | SEMIHARMONIC5 | X-RAY DIFFRACTION | t_sum_occupancies | | | | X-RAY DIFFRACTION | t_utility_distance | | | | X-RAY DIFFRACTION | t_utility_angle | | | | X-RAY DIFFRACTION | t_utility_torsion | | | | X-RAY DIFFRACTION | t_ideal_dist_contact | 4338 | SEMIHARMONIC4 | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | 解像度: 2.35→2.37 Å / Total num. of bins used: 51
| Rfactor | 反射数 | %反射 |
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Rfree | 0.3033 | - | 6.63 % |
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Rwork | 0.3172 | 563 | - |
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all | 0.3162 | 603 | - |
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obs | - | - | 99.01 % |
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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 | 3.5054 | -1.2747 | -0.1832 | 2.2006 | 0.4503 | 0.51 | 0.0759 | 0.2556 | 0.3263 | -0.0833 | -0.0621 | -0.3829 | -0.0737 | 0.1047 | -0.0138 | -0.093 | -0.0342 | 0.1058 | -0.1007 | 0.0611 | 0.1553 | -19.2433 | -0.3188 | -6.796 | 2 | 2.155 | -0.8993 | 0.1938 | 2.5248 | 0.364 | 1.1777 | -0.1163 | -0.3423 | 0.4165 | 0.3748 | -0.0143 | -0.3873 | 0.0163 | 0.1683 | 0.1306 | -0.0522 | -0.0506 | -0.0074 | -0.1147 | -0.0929 | 0.2104 | -22.5416 | 7.6845 | 10.9255 | 3 | 1.4198 | -0.0849 | -0.6042 | 1.1203 | 1.3726 | 1.7623 | 0.052 | 0.1256 | 0.374 | -0.0137 | -0.1417 | -0.0345 | -0.078 | -0.0418 | 0.0897 | 0.0063 | -0.0108 | 0.0733 | -0.1557 | 0.0253 | 0.2975 | -33.7237 | 8.7392 | 0.0874 | 4 | 1.6682 | -0.4802 | -0.1051 | 2.0452 | 0.9235 | 1.4659 | 0.0027 | 0.6369 | 0.3486 | -0.3153 | -0.1335 | 0.0082 | -0.1415 | -0.0301 | 0.1309 | -0.0457 | -0.0051 | 0.0853 | -0.1382 | 0.1607 | 0.1383 | -30.5701 | 5.1773 | -12.8835 | 5 | 2.06 | 2.3537 | -0.401 | 7.7532 | -0.5268 | 0.2772 | 0.1262 | -0.1983 | -0.0734 | -0.0966 | -0.0395 | -0.0856 | 0.1429 | -0.0402 | -0.0867 | 0.0931 | -0.018 | -0.0472 | 0.0013 | 0.0418 | -0.2065 | -27.7388 | 14.7217 | -42.9833 | 6 | 1.7965 | 0.4596 | -0.3093 | 3.0359 | -0.9388 | 1.0956 | 0.3593 | -0.433 | 0.2215 | 0.4304 | -0.2639 | -0.1391 | -0.1517 | -0.0915 | -0.0953 | 0.0609 | -0.1488 | -0.0064 | 0.0812 | -0.1123 | -0.2003 | -26.5106 | 28.4393 | -31.8687 | 7 | 2.3972 | 1.3075 | 0.3812 | 4.0704 | -0.7145 | 2.0774 | 0.1529 | 0.1669 | 0.0458 | -0.874 | -0.4096 | -0.7833 | 0.4815 | 0.4023 | 0.2567 | 0.0921 | 0.1361 | 0.149 | -0.0737 | 0.0069 | -0.1184 | -18.5162 | 23.958 | -52.0937 |
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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 | { A|42 - A|161 } | 2 | X-RAY DIFFRACTION | 2 | { A|162 - A|282 } | 3 | X-RAY DIFFRACTION | 3 | { A|283 - A|347 } | 4 | X-RAY DIFFRACTION | 4 | { A|348 - A|404 } | 5 | X-RAY DIFFRACTION | 5 | { B|42 - B|161 } | 6 | X-RAY DIFFRACTION | 6 | { B|162 - B|347 } | 7 | X-RAY DIFFRACTION | 7 | { B|348 - B|402 } |
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