ソフトウェア | 名称 | バージョン | 分類 |
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xia2 | 0.5.492データ削減 | DIALS | Xia2 0.5.492データ削減 | Aimless | Xia2 0.5.492データスケーリング | Coot | 0.8.9.236モデル構築 | PHASER | v1.13.2998位相決定 | PHENIX | v1.13.2998精密化 | | | | | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.55→90.42 Å / SU ML: 0.16 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 17.5 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.1727 | 4938 | 4.86 % |
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Rwork | 0.1471 | - | - |
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obs | 0.1484 | 101519 | 99.35 % |
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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: 1.55→90.42 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 4574 | 0 | 0 | 690 | 5264 |
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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_d0.005 | 5361 | X-RAY DIFFRACTION | f_angle_d0.811 | 7421 | X-RAY DIFFRACTION | f_dihedral_angle_d12.58 | 1975 | X-RAY DIFFRACTION | f_chiral_restr0.048 | 827 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1014 | | | | | |
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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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1.55-1.57 | 0.3018 | 122 | 0.2633 | 3166 | X-RAY DIFFRACTION | 99 | 1.57-1.59 | 0.2597 | 168 | 0.2468 | 3181 | X-RAY DIFFRACTION | 99 | 1.59-1.61 | 0.2414 | 157 | 0.2419 | 3201 | X-RAY DIFFRACTION | 99 | 1.61-1.63 | 0.275 | 136 | 0.2427 | 3231 | X-RAY DIFFRACTION | 99 | 1.63-1.65 | 0.258 | 144 | 0.2252 | 3232 | X-RAY DIFFRACTION | 99 | 1.65-1.67 | 0.2564 | 170 | 0.2268 | 3120 | X-RAY DIFFRACTION | 99 | 1.67-1.69 | 0.2445 | 186 | 0.2185 | 3177 | X-RAY DIFFRACTION | 99 | 1.69-1.72 | 0.2343 | 169 | 0.2086 | 3204 | X-RAY DIFFRACTION | 99 | 1.72-1.75 | 0.2186 | 170 | 0.2006 | 3150 | X-RAY DIFFRACTION | 99 | 1.75-1.77 | 0.2544 | 185 | 0.2053 | 3184 | X-RAY DIFFRACTION | 99 | 1.77-1.8 | 0.1967 | 172 | 0.194 | 3198 | X-RAY DIFFRACTION | 99 | 1.8-1.84 | 0.2271 | 142 | 0.1772 | 3218 | X-RAY DIFFRACTION | 99 | 1.84-1.87 | 0.1673 | 161 | 0.1649 | 3210 | X-RAY DIFFRACTION | 99 | 1.87-1.91 | 0.1814 | 175 | 0.1577 | 3191 | X-RAY DIFFRACTION | 99 | 1.91-1.95 | 0.1667 | 172 | 0.1489 | 3210 | X-RAY DIFFRACTION | 99 | 1.95-2 | 0.1586 | 174 | 0.1417 | 3203 | X-RAY DIFFRACTION | 99 | 2-2.05 | 0.1774 | 192 | 0.1433 | 3226 | X-RAY DIFFRACTION | 100 | 2.05-2.1 | 0.1712 | 161 | 0.1409 | 3226 | X-RAY DIFFRACTION | 100 | 2.1-2.17 | 0.1637 | 170 | 0.1317 | 3206 | X-RAY DIFFRACTION | 100 | 2.17-2.24 | 0.1705 | 165 | 0.1267 | 3239 | X-RAY DIFFRACTION | 100 | 2.24-2.32 | 0.1417 | 146 | 0.1254 | 3262 | X-RAY DIFFRACTION | 100 | 2.32-2.41 | 0.1652 | 152 | 0.1268 | 3243 | X-RAY DIFFRACTION | 100 | 2.41-2.52 | 0.1481 | 145 | 0.1265 | 3264 | X-RAY DIFFRACTION | 100 | 2.52-2.65 | 0.1542 | 144 | 0.1356 | 3270 | X-RAY DIFFRACTION | 100 | 2.65-2.82 | 0.1638 | 169 | 0.1388 | 3249 | X-RAY DIFFRACTION | 100 | 2.82-3.03 | 0.166 | 171 | 0.1423 | 3249 | X-RAY DIFFRACTION | 100 | 3.03-3.34 | 0.1528 | 176 | 0.1367 | 3239 | X-RAY DIFFRACTION | 100 | 3.34-3.82 | 0.1532 | 185 | 0.1246 | 3248 | X-RAY DIFFRACTION | 100 | 3.82-4.82 | 0.1377 | 176 | 0.114 | 3245 | X-RAY DIFFRACTION | 100 | 4.82-90.42 | 0.1795 | 183 | 0.1444 | 3339 | X-RAY DIFFRACTION | 100 |
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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 | 1.3223 | 0.2411 | 0.7737 | 1.5588 | 0.4857 | 2.6091 | 0.029 | -0.0048 | -0.0753 | 0.0519 | -0.0518 | -0.092 | 0.0637 | -0.0005 | 0.0232 | 0.1218 | -0.0044 | -0.0082 | 0.104 | 0.0074 | 0.1366 | 13.5077 | 4.8291 | 36.6507 | 2 | 1.0435 | -0.0976 | -0.0122 | 0.7938 | 0.0715 | 0.2629 | 0.0359 | 0.0775 | 0.0528 | -0.0171 | -0.0733 | 0.1157 | -0.0263 | -0.0617 | 0.0385 | 0.1439 | 0.0056 | -0.0184 | 0.1782 | -0.0076 | 0.1689 | -5.0701 | 11.5823 | 35.1288 | 3 | 1.6182 | -0.2449 | 0.5414 | 1.2046 | -0.3999 | 0.8091 | 0.0376 | -0.1686 | -0.0276 | 0.0564 | -0.0602 | 0.2074 | 0.0338 | -0.1089 | 0.0293 | 0.0977 | -0.0136 | 0.009 | 0.1552 | -0.0313 | 0.1438 | -8.154 | 13.7822 | 44.106 | 4 | 2.9061 | 1.0297 | 0.0555 | 0.5273 | 0.1193 | 0.186 | -0.0727 | -0.0342 | 0.3186 | -0.1466 | -0.0025 | 0.3495 | -0.0578 | -0.101 | 0.0658 | 0.1554 | 0.0172 | -0.0275 | 0.16 | -0.0291 | 0.231 | -3.3376 | 31.962 | 39.6945 | 5 | 1.6728 | -0.4009 | 0.3897 | 4.7643 | -1.8614 | 2.2352 | 0.0307 | -0.4053 | 0.3006 | 0.3205 | -0.0527 | 0.1781 | -0.1762 | -0.1648 | 0.0176 | 0.1235 | -0.0147 | 0.028 | 0.2201 | -0.0805 | 0.1905 | -7.0479 | 23.163 | 49.7815 | 6 | 0.9366 | 0.4262 | -0.0456 | 1.2448 | 0.0484 | 0.704 | 0.0485 | -0.1484 | 0.1162 | 0.0867 | -0.0736 | 0.0444 | -0.0561 | -0.0492 | 0.023 | 0.1419 | 0.0023 | -0.0085 | 0.1644 | -0.0285 | 0.1474 | 6.606 | 24.5397 | 46.317 | 7 | 0.624 | 0.0096 | -0.0013 | 1.0625 | 0.5759 | 1.1432 | 0.0235 | -0.0102 | -0.0151 | 0.0003 | 0.0102 | -0.0912 | -0.0422 | 0.0839 | -0.0334 | 0.1005 | -0.0022 | -0.012 | 0.1135 | -0.0061 | 0.1324 | 18.5661 | 16.4769 | 37.4396 | 8 | 1.2159 | 0.1203 | 0.5329 | 1.5808 | 0.6197 | 2.8186 | -0.0378 | 0.0502 | 0.1116 | -0.0249 | -0.0007 | -0.0768 | -0.0315 | 0.1093 | 0.0502 | 0.1649 | 0.0048 | 0.007 | 0.119 | 0.0113 | 0.1416 | 4.8251 | 11.5213 | 6.2029 | 9 | 1.3478 | 0.5364 | -0.282 | 1.2303 | -0.2407 | 0.7641 | 0.0832 | -0.2288 | 0.0244 | 0.2675 | -0.1126 | 0.3109 | 0.0238 | -0.097 | 0.0363 | 0.2663 | -0.0113 | 0.0698 | 0.2179 | -0.0104 | 0.2077 | -10.9725 | 4.9105 | 18.7249 | 10 | 0.82 | -0.087 | -0.2786 | 0.6425 | 0.5336 | 0.9461 | -0.025 | -0.0245 | -0.004 | 0.1357 | -0.0293 | 0.4049 | 0.0673 | -0.1683 | 0.044 | 0.1917 | -0.0061 | 0.0612 | 0.1953 | -0.0155 | 0.2508 | -16.1218 | -3.0345 | 13.0047 | 11 | 1.8679 | -0.7272 | -0.4545 | 1.3781 | 0.3044 | 1.1493 | -0.0318 | 0.1356 | -0.0431 | 0.0288 | -0.0238 | 0.2933 | 0.046 | -0.1663 | 0.0434 | 0.1691 | -0.0179 | -0.0014 | 0.1827 | -0.0192 | 0.2092 | -12.2256 | -4.7899 | 5.0665 | 12 | 5.8404 | -2.383 | 1.5829 | 2.2433 | -0.8646 | 1.8462 | -0.0322 | 0.22 | -0.2056 | -0.3045 | -0.082 | 0.3524 | 0.1189 | -0.0827 | 0.1323 | 0.2179 | -0.0258 | -0.0198 | 0.162 | -0.0313 | 0.2114 | -10.7077 | -14.4043 | 0.3086 | 13 | 1.2783 | 0.5273 | 0.5312 | 1.2284 | 0.4925 | 0.9875 | 0.0244 | 0.0982 | -0.0219 | -0.0862 | 0.0268 | -0.0416 | 0.0365 | 0.0624 | -0.0552 | 0.1635 | 0.012 | 0.0152 | 0.1358 | -0.0066 | 0.1186 | 6.7289 | -1.3331 | 3.4937 |
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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 3 through 45 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 46 through 100 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 101 through 130 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 131 through 149 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 150 through 163 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 164 through 213 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 214 through 303 )8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 3 through 45 )9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resid 46 through 100 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 101 through 149 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 150 through 181 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 182 through 196 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 197 through 303 ) | | | | | | | | | | | | |
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