ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | (PHENIX.REFINE: 1.8.1_1168)精密化 | XDS | | データ削減 | XSCALE | | データスケーリング | MOLREP | | 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: 2.101→50.206 Å / SU ML: 0.23 / σ(F): 2.02 / 位相誤差: 26.71 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2395 | 1079 | 5.1 % |
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Rwork | 0.187 | - | - |
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obs | 0.1899 | 21018 | 98.59 % |
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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: 2.101→50.206 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 2588 | 0 | 1 | 93 | 2682 |
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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_d0.006 | 2635 | X-RAY DIFFRACTION | f_angle_d1.069 | 3597 | X-RAY DIFFRACTION | f_dihedral_angle_d14.665 | 907 | X-RAY DIFFRACTION | f_chiral_restr0.076 | 433 | X-RAY DIFFRACTION | f_plane_restr0.003 | 462 | | | | | |
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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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2.1013-2.197 | 0.3374 | 116 | 0.2626 | 2378 | X-RAY DIFFRACTION | 95 | 2.197-2.3128 | 0.3069 | 120 | 0.2504 | 2512 | X-RAY DIFFRACTION | 100 | 2.3128-2.4577 | 0.2871 | 135 | 0.2439 | 2497 | X-RAY DIFFRACTION | 99 | 2.4577-2.6474 | 0.3066 | 129 | 0.231 | 2512 | X-RAY DIFFRACTION | 99 | 2.6474-2.9138 | 0.2737 | 167 | 0.2043 | 2481 | X-RAY DIFFRACTION | 100 | 2.9138-3.3354 | 0.2619 | 137 | 0.1853 | 2529 | X-RAY DIFFRACTION | 100 | 3.3354-4.2019 | 0.2218 | 140 | 0.1604 | 2523 | X-RAY DIFFRACTION | 99 | 4.2019-50.2203 | 0.1899 | 135 | 0.1615 | 2507 | X-RAY DIFFRACTION | 97 |
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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 | 1.4039 | 0.522 | 0.9849 | 0.5015 | 0.304 | 0.6635 | -0.1901 | 0.2351 | -0.1785 | -0.3472 | -0.1674 | 0.3253 | -0.2093 | -0.1822 | -0.0009 | 0.4588 | -0.0489 | -0.0024 | 0.3111 | 0.0332 | 0.4496 | 6.5527 | 0.3375 | 24.2616 | 2 | 0.6308 | 0.5746 | 0.0667 | 0.6292 | -0.2136 | 0.5473 | -0.1262 | -0.1045 | 0.1666 | 0.356 | 0.078 | -0.3423 | -0.4331 | 0.2272 | 0.0002 | 0.3771 | -0.016 | -0.0594 | 0.3151 | 0.0003 | 0.4319 | 11.4397 | 2.0493 | 32.0664 | 3 | 0.3303 | -0.0209 | 0.1308 | 0.1288 | 0.0917 | 0.837 | -1 | 0.4945 | 0.4507 | -0.8117 | 0.6058 | 0.0968 | 0.181 | 0.2394 | -0.1146 | 0.4738 | -0.019 | -0.0547 | 0.4134 | -0.0025 | 0.6172 | 15.8681 | -7.473 | 18.28 | 4 | 0.9351 | 0.1703 | 0.6175 | 0.7761 | 0.4439 | 0.4758 | 0.0082 | -0.1674 | 0.2641 | 0.0999 | 0.0268 | -0.0285 | -0.1622 | 0.2459 | 0.0004 | 0.4828 | -0.0385 | -0.0227 | 0.3374 | 0.053 | 0.3603 | 6.982 | -10.7163 | 23.0421 | 5 | 1.917 | -0.017 | 0.1815 | 1.6408 | -0.2638 | 1.6986 | -0.0722 | 0.1878 | 0.1245 | -0.1224 | 0.0854 | -0.0081 | 0.0304 | -0.0127 | 0.0002 | 0.2998 | -0.0032 | -0.0038 | 0.2442 | 0.0317 | 0.2644 | 2.8625 | -14.0718 | 19.266 | 6 | 1.572 | 0.6257 | -0.3764 | 0.9711 | -0.9431 | 0.8535 | -0.3103 | 0.4316 | 0.1243 | -0.4623 | 0.1209 | 0.2187 | -0.3798 | -0.2496 | -0.0001 | 0.5191 | 0.012 | -0.0269 | 0.4739 | 0.0098 | 0.4533 | -2.7823 | -21.0248 | 13.9601 | 7 | 2.1754 | -1.3144 | -0.0849 | 0.9371 | 0.4541 | 0.6132 | 0.4006 | 0.188 | -0.5942 | -0.4891 | -0.4468 | -0.1994 | 0.1431 | 0.019 | 0.0006 | 0.4852 | 0.1037 | 0.001 | 0.5656 | 0.0006 | 0.4357 | -9.9702 | -14.3275 | 11.8789 | 8 | 1.0214 | -1.3072 | 0.4081 | 2.0287 | -0.6744 | 0.1807 | 0.543 | 0.2444 | -0.3082 | -0.7207 | -0.5224 | 0.1367 | -0.0958 | 0.0707 | -0.0021 | 0.6175 | 0.1054 | -0.0602 | 0.6128 | -0.1227 | 0.4479 | -17.7404 | -7.4774 | 3.3701 | 9 | 0.1452 | 0.2018 | 0.1544 | 0.2714 | 0.2238 | 0.17 | 0.3006 | 0.6534 | 0.0674 | -0.0079 | -0.089 | -0.0682 | 0.2762 | -0.7766 | 0.0018 | 0.4258 | 0.0606 | 0.0612 | 0.6111 | -0.1307 | 0.3478 | -18.1788 | 4.6971 | 7.5328 | 10 | 4.7463 | 2.6339 | -1.7837 | 1.6806 | -0.8443 | 0.8364 | 0.6597 | 0.3959 | 0.3268 | -0.4861 | -0.4531 | 0.9182 | -0.6631 | 0.4141 | -0.0475 | 0.3484 | 0.1274 | -0.0456 | 0.6815 | -0.0939 | 0.4411 | -16.2355 | 8.2237 | -1.0151 | 11 | 0.8114 | -0.8267 | -0.3326 | 0.824 | 0.4329 | 0.3775 | 0.2522 | 0.4506 | -0.2628 | -0.9375 | -0.5503 | -0.0165 | 0.1032 | 0.4473 | -0.0028 | 0.5694 | 0.09 | -0.1051 | 0.6483 | -0.0965 | 0.3915 | -23.7117 | 7.6804 | 1.3431 | 12 | 1.2872 | 0.5596 | 0.6952 | 3.8162 | 0.2327 | 2.005 | 0.8085 | 0.1684 | -0.5154 | -0.9357 | -0.9137 | -0.8931 | 2.2824 | 1.4274 | 0.4097 | 0.4316 | 0.2293 | 0.1018 | 1.0225 | 0.0581 | 0.1813 | -8.5266 | 9.9367 | 3.3233 | 13 | 0.2727 | -0.001 | 0.1354 | 0.3914 | 0.0029 | 0.054 | 0.1949 | 0.9932 | 0.2898 | -0.4679 | -0.1861 | 0.2836 | -0.0677 | -0.3298 | -0.0006 | 0.3249 | -0.0056 | 0.0496 | 0.5312 | -0.0021 | 0.2666 | -14.0973 | 12.9707 | 12.2566 | 14 | 6.2293 | -0.5543 | -1.8625 | 0.5684 | 0.523 | 0.8731 | 0.001 | 1.2692 | 0.3459 | -0.4274 | -0.6579 | -0.0466 | -0.1541 | 0.2668 | -1.0902 | 0.2811 | -0.0078 | 0.2209 | 1.3289 | 0.2188 | 0.4775 | -3.7729 | 16.99 | 2.903 | 15 | 0.0045 | 0.0319 | -0.0405 | 0.0296 | -0.0911 | 0.1124 | 0.1587 | 0.2014 | -0.2922 | -0.1791 | -0.4154 | 0.111 | -0.0842 | 0.4847 | -0.0012 | 0.3678 | 0.1196 | -0.026 | 0.6435 | 0.0029 | 0.4381 | -18.4646 | 16.4887 | 7.7712 | 16 | 1.0812 | 1.9633 | -0.1935 | 3.5202 | -0.326 | 0.0288 | 0.4126 | 0.2093 | 0.2258 | 0.6742 | 0.5383 | 0.8509 | -1.0192 | -0.3479 | 0.1102 | 0.5102 | -0.0764 | -0.101 | 0.6088 | 0.1746 | 0.4851 | -11.5546 | 22.1054 | 8.7714 | 17 | 0.8862 | 0.2242 | 0.3338 | 0.8387 | 0.1096 | 0.6194 | -0.313 | 0.0827 | -0.0096 | 0.0341 | 0.2379 | -0.0255 | 0.0186 | -0.0807 | -0.0003 | 0.3657 | -0.006 | 0.0234 | 0.4282 | 0.0056 | 0.399 | -4.5704 | 15.8115 | 15.7872 | 18 | 0.9835 | -1.1196 | 1.2933 | 1.1546 | -1.2549 | 1.3359 | 0.0375 | 0.1623 | -0.0903 | -0.2557 | -0.0229 | -0.0608 | -0.0874 | 0.464 | -0.0001 | 0.3967 | -0.0311 | 0.0766 | 0.3625 | -0.0099 | 0.43 | 4.7243 | 13.7226 | 23.4933 |
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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 62 THROUGH 79 )2 | X-RAY DIFFRACTION | 2 | CHAIN A AND (RESID 80 THROUGH 96 )3 | X-RAY DIFFRACTION | 3 | CHAIN A AND (RESID 97 THROUGH 115 )4 | X-RAY DIFFRACTION | 4 | CHAIN A AND (RESID 116 THROUGH 135 )5 | X-RAY DIFFRACTION | 5 | CHAIN A AND (RESID 136 THROUGH 175 )6 | X-RAY DIFFRACTION | 6 | CHAIN A AND (RESID 176 THROUGH 191 )7 | X-RAY DIFFRACTION | 7 | CHAIN C AND (RESID 229 THROUGH 276 )8 | X-RAY DIFFRACTION | 8 | CHAIN C AND (RESID 277 THROUGH 322 )9 | X-RAY DIFFRACTION | 9 | CHAIN B AND (RESID 113 THROUGH 125 )10 | X-RAY DIFFRACTION | 10 | CHAIN B AND (RESID 126 THROUGH 135 )11 | X-RAY DIFFRACTION | 11 | CHAIN B AND (RESID 136 THROUGH 146 )12 | X-RAY DIFFRACTION | 12 | CHAIN B AND (RESID 147 THROUGH 155 )13 | X-RAY DIFFRACTION | 13 | CHAIN B AND (RESID 156 THROUGH 165 )14 | X-RAY DIFFRACTION | 14 | CHAIN B AND (RESID 166 THROUGH 170 )15 | X-RAY DIFFRACTION | 15 | CHAIN B AND (RESID 171 THROUGH 180 )16 | X-RAY DIFFRACTION | 16 | CHAIN B | | | | | | | | | | | | | | | |
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