ソフトウェア | 名称 | バージョン | 分類 |
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SCALA | 3.3.20データスケーリング | PHENIX | | 精密化 | PDB_EXTRACT | 3.2 | データ抽出 | XDS | | データ削減 | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.2→45.237 Å / SU ML: 0.28 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 23.81
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2265 | 4811 | 5 % |
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Rwork | 0.1815 | - | - |
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obs | 0.1838 | 96188 | 99.53 % |
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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 |
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原子変位パラメータ | Biso max: 197.48 Å2 / Biso mean: 64.7478 Å2 / Biso min: 19.12 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.2→45.237 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 10804 | 0 | 45 | 421 | 11270 |
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Biso mean | - | - | 49.24 | 53.25 | - |
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残基数 | - | - | - | - | 1398 |
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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 | 11053 | X-RAY DIFFRACTION | f_angle_d1.141 | 14976 | X-RAY DIFFRACTION | f_chiral_restr0.046 | 1593 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1979 | X-RAY DIFFRACTION | f_dihedral_angle_d14.051 | 4020 | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.2-2.225 | 0.3552 | 148 | 0.2821 | 2977 | 3125 | 99 | 2.225-2.2512 | 0.3393 | 169 | 0.2736 | 2949 | 3118 | 98 | 2.2512-2.2786 | 0.3157 | 151 | 0.2712 | 3004 | 3155 | 99 | 2.2786-2.3075 | 0.334 | 150 | 0.2474 | 3007 | 3157 | 100 | 2.3075-2.3378 | 0.3132 | 184 | 0.2395 | 3010 | 3194 | 100 | 2.3378-2.3699 | 0.2522 | 169 | 0.2336 | 3018 | 3187 | 100 | 2.3699-2.4037 | 0.2599 | 154 | 0.2263 | 3006 | 3160 | 100 | 2.4037-2.4396 | 0.3035 | 171 | 0.2277 | 3050 | 3221 | 100 | 2.4396-2.4777 | 0.3014 | 156 | 0.2202 | 3012 | 3168 | 100 | 2.4777-2.5183 | 0.3135 | 157 | 0.22 | 3020 | 3177 | 100 | 2.5183-2.5618 | 0.2875 | 166 | 0.2143 | 3048 | 3214 | 100 | 2.5618-2.6083 | 0.2675 | 149 | 0.2009 | 3015 | 3164 | 100 | 2.6083-2.6585 | 0.2563 | 166 | 0.201 | 3047 | 3213 | 100 | 2.6585-2.7127 | 0.2445 | 173 | 0.1997 | 3011 | 3184 | 99 | 2.7127-2.7717 | 0.2428 | 155 | 0.1897 | 2981 | 3136 | 99 | 2.7717-2.8362 | 0.2693 | 155 | 0.1919 | 3039 | 3194 | 100 | 2.8362-2.9071 | 0.2428 | 145 | 0.1921 | 3078 | 3223 | 100 | 2.9071-2.9857 | 0.2521 | 152 | 0.1937 | 3043 | 3195 | 100 | 2.9857-3.0735 | 0.2372 | 149 | 0.1989 | 3056 | 3205 | 100 | 3.0735-3.1727 | 0.2691 | 159 | 0.2117 | 3060 | 3219 | 100 | 3.1727-3.2861 | 0.2623 | 169 | 0.2142 | 3048 | 3217 | 100 | 3.2861-3.4176 | 0.2649 | 157 | 0.1965 | 3055 | 3212 | 100 | 3.4176-3.5731 | 0.2324 | 170 | 0.185 | 3047 | 3217 | 99 | 3.5731-3.7614 | 0.2157 | 131 | 0.1795 | 3077 | 3208 | 100 | 3.7614-3.9969 | 0.2156 | 189 | 0.1657 | 3066 | 3255 | 100 | 3.9969-4.3053 | 0.1647 | 147 | 0.1489 | 3072 | 3219 | 100 | 4.3053-4.7381 | 0.1617 | 167 | 0.1327 | 3099 | 3266 | 100 | 4.7381-5.4228 | 0.1964 | 152 | 0.1524 | 3112 | 3264 | 99 | 5.4228-6.8284 | 0.2257 | 184 | 0.1753 | 3122 | 3306 | 99 | 6.8284-45.2463 | 0.1752 | 167 | 0.1569 | 3248 | 3415 | 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 | 2.3184 | -0.8795 | -0.4286 | 2.1797 | 0.3815 | 1.2044 | -0.135 | -0.455 | -0.0875 | 0.4505 | 0.004 | -0.0249 | 0.0114 | 0.1817 | 0.1077 | 0.3467 | -0.062 | -0.0277 | 0.4064 | 0.0085 | 0.2687 | 13.8793 | -20.5638 | -12.8541 | 2 | 1.3439 | -0.3435 | -0.4484 | 1.5262 | -0.0256 | 1.3565 | -0.1005 | -0.1254 | -0.1884 | 0.243 | -0.1036 | 0.1521 | 0.1801 | -0.0517 | 0.202 | 0.309 | -0.0423 | 0.0464 | 0.3335 | -0.0233 | 0.2855 | 4.1758 | -28.2664 | -20.8753 | 3 | 2.2895 | -0.4756 | -1.6386 | 0.8502 | 0.5159 | 1.5311 | -0.3004 | -0.4052 | -0.4163 | 0.3879 | -0.0382 | 0.2455 | 0.542 | -0.0433 | 0.3481 | 0.6058 | -0.0832 | 0.1713 | 0.5923 | 0.0702 | 0.562 | -9.4475 | -41.6857 | -1.5032 | 4 | 1.301 | -0.0793 | -0.0538 | 2.1394 | 0.2641 | 1.9488 | 0.0171 | 0.0328 | 0.2089 | -0.0824 | -0.1279 | 0.1161 | -0.3826 | -0.0845 | 0.109 | 0.2738 | -0.0026 | 0.0034 | 0.2766 | -0.0476 | 0.2617 | 2.9445 | -12.1073 | -29.4419 | 5 | 2.2191 | -1.3466 | 0.4771 | 5.5668 | 0.2966 | 1.2494 | 0.2512 | 0.4153 | -0.392 | -0.981 | -0.3653 | 1.592 | 0.0523 | -0.2053 | 0.0448 | 0.4872 | 0.0305 | -0.3203 | 0.4729 | -0.1289 | 0.6699 | -29.0039 | -27.3253 | -64.8672 | 6 | 2.9002 | -0.6895 | -0.2867 | 8.0122 | -0.9473 | 2.1074 | -0.0893 | -0.2763 | 0.1229 | 0.9825 | 0.008 | 1.7286 | -0.4669 | -0.2022 | 0.0409 | 0.3953 | 0.0003 | 0.098 | 0.4242 | -0.0925 | 0.6909 | -32.8841 | -8.2427 | -48.505 | 7 | 2.1628 | 0.3304 | -0.1457 | 2.5877 | -1.5917 | 1.2262 | 0.1063 | -0.371 | -0.6531 | 0.1068 | 0.0289 | 2.1091 | 0.2854 | -0.3969 | -0.3158 | 0.8753 | -0.211 | 0.5226 | 0.9217 | 0.0671 | 2.3772 | -49.7385 | -39.1691 | -42.7316 | 8 | 2.3187 | -1.4108 | 0.4537 | 5.3244 | 0.2783 | 1.2424 | 0.1428 | 0.2595 | -0.065 | -0.5324 | -0.1891 | 0.5804 | -0.0311 | -0.0329 | 0.0509 | 0.295 | 0.0112 | -0.0688 | 0.3354 | -0.0308 | 0.251 | -18.9474 | -24.3639 | -57.6529 | 9 | 2 | -8.3191 | 1.7835 | 2.0033 | 3.0921 | 2.0007 | -0.2307 | -0.8021 | -0.1696 | 0.8608 | -0.0894 | 0.3773 | -0.3791 | -0.2808 | 0.3261 | 0.2841 | -0.0284 | 0.0837 | 0.5597 | -0.216 | 0.5587 | -0.1369 | -22.994 | -22.5044 | 10 | 5.3149 | -9.5117 | 6.3006 | 2.0029 | -9.67 | 7.7087 | 0.0327 | -0.0842 | -0.5493 | -0.2518 | 0.8152 | 1.81 | 0.0984 | -1.118 | -0.8911 | 0.3808 | 0.0415 | 0.0091 | 0.4326 | 0.0009 | 0.4921 | -24.1017 | -27.3425 | -54.0912 |
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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 21 through 184 )A21 - 184 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 185 through 399 )A185 - 399 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 400 through 560 )A400 - 560 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 561 through 723 )A561 - 723 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 21 through 323 )B21 - 323 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 324 through 385 )B324 - 385 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 386 through 521 )B386 - 521 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 522 through 718 )B522 - 718 | 9 | X-RAY DIFFRACTION | 9 | chain 'D' and (resid 1 through 2 )D1 - 2 | 10 | X-RAY DIFFRACTION | 10 | chain 'E' and (resid 1 through 2 )E1 - 2 | | | | | | | | | | | | | | | | | | | | |
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