ソフトウェア | 名称 | バージョン | 分類 |
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PHENIX | 1.11.1_2575精密化 | PDB_EXTRACT | 3.25 | データ抽出 | DENZO | | データ削減 | SCALEPACK | | データスケーリング | PHASER | | 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: 2C3F 解像度: 2.21→38.609 Å / SU ML: 0.26 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 25.95 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2368 | 2383 | 4.77 % |
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Rwork | 0.2127 | 47657 | - |
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obs | - | 50040 | 99.55 % |
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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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原子変位パラメータ | Biso max: 144.15 Å2 / Biso mean: 42.9976 Å2 / Biso min: 16.18 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.21→38.609 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6100 | 0 | 1 | 282 | 6383 |
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Biso mean | - | - | 65.83 | 41.79 | - |
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残基数 | - | - | - | - | 815 |
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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 | 6181 | X-RAY DIFFRACTION | f_angle_d0.997 | 8299 | X-RAY DIFFRACTION | f_chiral_restr0.055 | 942 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1074 | X-RAY DIFFRACTION | f_dihedral_angle_d7.516 | 3817 | | | | | |
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Refine LS restraints NCS | Ens-ID | Dom-ID | Auth asym-ID | 数 | Refine-ID | Rms | タイプ |
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1 | 1 | A3806 | X-RAY DIFFRACTION | 13.761 | TORSIONAL1 | 2 | B3806 | X-RAY DIFFRACTION | 13.761 | TORSIONAL1 | 3 | C3806 | X-RAY DIFFRACTION | 13.761 | TORSIONAL | | | | | |
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LS精密化 シェル | 解像度: 2.21→2.289 Å / Rfactor Rfree error: 0
| Rfactor | 反射数 | %反射 |
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Rfree | 0.3134 | 209 | - |
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Rwork | 0.2987 | 4729 | - |
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obs | - | - | 99 % |
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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 | -0.0065 | -0.0014 | 0.1344 | -0.0826 | -0.0528 | 2.3035 | 0.06 | 0.2421 | 0.259 | -0.1622 | 0.059 | -0.1874 | 0.0773 | 0.1844 | 0.0052 | 0.7615 | -0.0807 | 0.1032 | 0.6657 | 0.0469 | 0.4188 | 30.4141 | 17.968 | -7.8196 | 2 | 0.2606 | 0.0603 | 0.044 | 0.3676 | 0.1354 | 1.4757 | -0.0185 | 0.0778 | -0.0016 | -0.1041 | 0.0489 | -0.0653 | 0.0007 | 0.001 | 0.0044 | 0.2748 | 0.0175 | 0.0005 | 0.2039 | 0.026 | 0.3824 | 29.2768 | 25.2298 | 43.1277 | 3 | 0.469 | 0.0241 | 0.2553 | 1.2042 | 0.3606 | 1.9855 | 0.0122 | -0.1577 | -0.0247 | 0.1276 | -0.0422 | 0.0052 | 0.1097 | -0.023 | 0.0069 | 0.1639 | 0.0198 | -0.0274 | 0.1899 | 0.0425 | 0.3088 | 30.1968 | 25.0208 | 74.2821 | 4 | 0.0889 | -0.124 | 0.6871 | 0.654 | -0.2806 | 1.8471 | -0.1351 | -0.1502 | 0.0612 | 0.1831 | 0.1243 | 0.0553 | -0.2577 | -0.2119 | 0.0345 | 0.312 | 0.0853 | -0.0285 | 0.5246 | -0.0342 | 0.356 | 27.9115 | 36.0389 | 111.7553 | 5 | 0.397 | -0.2162 | -0.4454 | 0.0945 | 0.1294 | 1.6703 | -0.0897 | 0.5086 | 0.3555 | -0.1055 | 0.2993 | 0.417 | 0.172 | -0.68 | -0.0206 | 0.8437 | -0.2092 | -0.0814 | 0.9225 | 0.1349 | 0.3628 | 27.1928 | 20.4234 | -6.3617 | 6 | 0.4785 | 0.0866 | 0.0252 | 0.4281 | -0.0203 | 1.1038 | -0.0202 | 0.0044 | 0.0465 | -0.1263 | 0.04 | -0.0224 | 0.05 | 0.0084 | 0.0098 | 0.2734 | 0.0156 | -0.0099 | 0.1717 | 0.0092 | 0.3703 | 28.4894 | 24.392 | 43.235 | 7 | 1.2885 | 0.1163 | -0.3234 | 0.6957 | 0.041 | 1.9952 | -0.0338 | -0.1834 | 0.0541 | 0.0518 | 0.012 | -0.0798 | -0.0645 | 0.0543 | 0.0198 | 0.1969 | 0.0261 | -0.0251 | 0.2436 | 0.0168 | 0.3379 | 31.5148 | 30.2476 | 73.6272 | 8 | -0.134 | -0.6424 | 0.6753 | 1.0874 | 0.3221 | 1.6377 | -0.1128 | -0.251 | 0.0277 | 0.255 | 0.1373 | 0.0103 | 0.0262 | -0.2958 | 0.0053 | 0.3105 | 0.045 | -0.0477 | 0.6066 | 0.0069 | 0.3749 | 28.1671 | 29.0892 | 112.5703 | 9 | 0.0117 | 0.0661 | 0.0967 | 0.8487 | 0.8797 | 2.3011 | 0.4701 | 0.2061 | -0.4935 | 0.1624 | -0.1453 | -0.1034 | 0.4425 | 0.2608 | -0.0147 | 1.1602 | 0.1205 | 0.073 | 0.8749 | -0.0036 | 0.7885 | 32.932 | 12.3468 | -19.8512 | 10 | 0.0128 | -0.0182 | -0.1367 | 0.013 | 0.2179 | 2.1132 | 0.0298 | 0.3464 | -0.0744 | -0.698 | 0.2053 | 0.302 | 0.5253 | -0.7312 | -0.0159 | 1.0019 | -0.0672 | -0.0303 | 0.5765 | -0.0231 | 0.3141 | 23.4896 | 18.2824 | 1.5604 | 11 | 0.9227 | 0.6542 | 0.4719 | 0.4685 | 0.1958 | 2.2117 | -0.0636 | 0.1584 | -0.0973 | -0.4009 | 0.1324 | -0.3556 | -0.0672 | 0.2619 | -0.0032 | 0.3734 | 0.0108 | 0.0344 | 0.2035 | -0.0083 | 0.3593 | 33.984 | 24.2098 | 28.6359 | 12 | 0.8762 | 0.1281 | 0.3861 | 1.0708 | 0.1057 | 1.6086 | 0.0072 | -0.0239 | -0.0888 | -0.1144 | 0.0371 | 0.0117 | 0.0776 | -0.1772 | -0.007 | 0.2327 | 0.0042 | 0.0016 | 0.1683 | 0.0256 | 0.3569 | 24.9481 | 23.7736 | 46.7212 | 13 | 0.5764 | 0.314 | 0.5775 | 1.3361 | -0.1903 | 1.8365 | -0.0567 | -0.1254 | 0.1032 | 0.0278 | 0.0675 | -0.0521 | -0.004 | -0.2752 | 0.0011 | 0.1286 | 0.0268 | 0.0183 | 0.206 | 0.0164 | 0.2959 | 24.8336 | 29.3809 | 65.0438 | 14 | 0.817 | -0.7941 | -0.3394 | 1.3998 | 0.0382 | 1.5734 | -0.0603 | -0.2147 | -0.1307 | -0.0531 | 0.2326 | -0.0363 | 0.4392 | -0.2366 | 0.028 | 0.3257 | -0.0207 | -0.0329 | 0.2102 | 0.0766 | 0.3738 | 26.7532 | 11.9025 | 71.6399 | 15 | 0.6541 | 0.1808 | -0.1886 | 0.682 | 0.6583 | 2.3407 | 0.017 | -0.1376 | -0.0721 | 0.0573 | -0.0652 | -0.0532 | -0.3484 | 0.1672 | -0.0105 | 0.2126 | -0.0041 | -0.0426 | 0.3506 | 0.0339 | 0.3606 | 32.6601 | 34.2928 | 86.7315 | 16 | 1.7183 | -0.1637 | 0.3317 | 1.4737 | 0.0531 | 2.1382 | -0.1174 | 0.2038 | 0.268 | 0.2527 | 0.0901 | -0.1568 | -0.6733 | 0.51 | 0.0004 | 0.3894 | 0.0982 | -0.0435 | 0.5111 | -0.009 | 0.4212 | 36.4002 | 32.7358 | 124.431 |
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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 105 through 135 )A105 - 135 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 136 through 255 )A136 - 255 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 256 through 327 )A256 - 327 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 328 through 377 )A328 - 377 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 107 through 135 )B107 - 135 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 136 through 255 )B136 - 255 | 7 | X-RAY DIFFRACTION | 7 | chain 'B' and (resid 256 through 327 )B256 - 327 | 8 | X-RAY DIFFRACTION | 8 | chain 'B' and (resid 328 through 377 )B328 - 377 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 107 through 116 )C107 - 116 | 10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 117 through 135 )C117 - 135 | 11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 136 through 175 )C136 - 175 | 12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 176 through 235 )C176 - 235 | 13 | X-RAY DIFFRACTION | 13 | chain 'C' and (resid 236 through 275 )C | | | | | | | | | | | | | | | | | | | | | | | | | |
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