ソフトウェア | 名称 | バージョン | 分類 |
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XDS | | データ削減 | PHENIX | | 精密化 | PDB_EXTRACT | 3.15 | データ抽出 | XSCALE | | 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: PDB entry 4OOS was used for GII.10 P domain (molecule 1) and recently deposited PDB entry 4X7E for Nano-85 (molecule 2) 解像度: 2.15→46.79 Å / SU ML: 0.28 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 25.97 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2379 | 2489 | 5 % |
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Rwork | 0.1955 | 47249 | - |
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obs | 0.1975 | 49738 | 99.42 % |
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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: 104.22 Å2 / Biso mean: 39.688 Å2 / Biso min: 20 Å2 |
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精密化ステップ | サイクル: final / 解像度: 2.15→46.79 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 6340 | 0 | 8 | 419 | 6767 |
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Biso mean | - | - | 32.11 | 36.55 | - |
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残基数 | - | - | - | - | 839 |
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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_d0.012 | 6544 | X-RAY DIFFRACTION | f_angle_d1.264 | 8937 | X-RAY DIFFRACTION | f_chiral_restr0.057 | 982 | X-RAY DIFFRACTION | f_plane_restr0.008 | 1187 | X-RAY DIFFRACTION | f_dihedral_angle_d13.713 | 2298 | | | | | |
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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 | A2788 | X-RAY DIFFRACTION | 8.187 | TORSIONAL1 | 2 | B2788 | X-RAY DIFFRACTION | 8.187 | TORSIONAL2 | 1 | C789 | X-RAY DIFFRACTION | 8.187 | TORSIONAL2 | 2 | D789 | X-RAY DIFFRACTION | 8.187 | TORSIONAL | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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2.1501-2.1915 | 0.3405 | 134 | 0.3071 | 2535 | 2669 | 98 | 2.1915-2.2362 | 0.3124 | 137 | 0.2789 | 2609 | 2746 | 100 | 2.2362-2.2849 | 0.3117 | 137 | 0.2669 | 2605 | 2742 | 100 | 2.2849-2.338 | 0.333 | 138 | 0.2531 | 2610 | 2748 | 100 | 2.338-2.3965 | 0.3021 | 136 | 0.2417 | 2589 | 2725 | 100 | 2.3965-2.4613 | 0.2779 | 136 | 0.2375 | 2576 | 2712 | 100 | 2.4613-2.5337 | 0.2999 | 138 | 0.2415 | 2622 | 2760 | 99 | 2.5337-2.6155 | 0.2593 | 136 | 0.2218 | 2577 | 2713 | 99 | 2.6155-2.7089 | 0.2864 | 136 | 0.2252 | 2602 | 2738 | 100 | 2.7089-2.8174 | 0.2544 | 139 | 0.2243 | 2630 | 2769 | 100 | 2.8174-2.9456 | 0.2806 | 138 | 0.2217 | 2627 | 2765 | 100 | 2.9456-3.1008 | 0.2754 | 137 | 0.2085 | 2591 | 2728 | 100 | 3.1008-3.2951 | 0.2403 | 137 | 0.1945 | 2611 | 2748 | 99 | 3.2951-3.5494 | 0.2533 | 140 | 0.1853 | 2648 | 2788 | 99 | 3.5494-3.9064 | 0.2014 | 140 | 0.17 | 2668 | 2808 | 100 | 3.9064-4.4713 | 0.1712 | 140 | 0.1479 | 2654 | 2794 | 99 | 4.4713-5.6319 | 0.1873 | 142 | 0.1503 | 2681 | 2823 | 99 | 5.6319-46.8011 | 0.2119 | 148 | 0.1821 | 2814 | 2962 | 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 | 3.0012 | 0.2479 | 0.6555 | 0.699 | -0.1957 | 1.135 | 0.1125 | -0.0541 | -0.2689 | -0.0719 | 0.001 | 0.2016 | 0.1766 | -0.1744 | -0.1082 | 0.2865 | -0.0316 | -0.0245 | 0.2054 | 0.0091 | 0.4152 | 7.9257 | -8.6123 | 139.8875 | 2 | 0.4749 | -0.8599 | 0.437 | 2.0246 | -0.6429 | 2.0548 | 0.0082 | 0.2107 | -0.1055 | -0.1993 | 0.119 | 0.3301 | 0.2218 | -0.2835 | -0.148 | 0.3046 | -0.0895 | -0.071 | 0.3821 | 0.0151 | 0.5369 | -5.8755 | -9.7945 | 130.18 | 3 | 2.235 | 0.2172 | -0.0527 | 0.8554 | -0.1178 | 0.9591 | 0.027 | -0.3231 | -0.2267 | 0.0789 | -0.0086 | 0.0006 | 0.0979 | -0.0157 | -0.0073 | 0.2529 | -0.0112 | -0.0172 | 0.1985 | 0.0326 | 0.329 | 14.3836 | -9.7667 | 148.9918 | 4 | 2.4396 | -0.0168 | -1.0678 | 1.3196 | 0.4336 | 1.8386 | 0.0619 | 0.1288 | 0.0843 | 0.0557 | 0.0422 | 0.1016 | -0.1163 | -0.1083 | -0.1212 | 0.2714 | 0.0061 | -0.0265 | 0.1977 | 0.0243 | 0.33 | 7.8162 | 12.2493 | 136.2114 | 5 | 1.4219 | 0.6463 | -0.7356 | 1.0574 | -0.4619 | 1.4633 | 0.0076 | 0.1667 | 0.3441 | 0.0256 | 0.1098 | 0.315 | -0.0933 | -0.2167 | -0.1385 | 0.2447 | 0.0215 | 0.0095 | 0.277 | 0.0466 | 0.4559 | -2.1411 | 14.8022 | 135.9276 | 6 | 3.3227 | -0.0054 | 0.4708 | 1.247 | -0.1146 | 1.6299 | -0.0136 | 0.629 | -0.1811 | -0.2259 | 0.1114 | -0.1486 | 0.0559 | 0.1358 | -0.0658 | 0.2728 | -0.0349 | 0.0036 | 0.2792 | -0.0512 | 0.2844 | 18.5288 | 7.7919 | 120.4357 | 7 | 1.9242 | -0.1132 | 1.7045 | 3.6468 | -3.4899 | 5.3699 | -0.3464 | 0.1312 | 0.9449 | -0.573 | 0.2389 | -0.335 | 0.5511 | -0.5247 | 0.2338 | 0.5115 | -0.0676 | 0.1268 | 1.4591 | 0.0253 | 0.6164 | 48.2761 | 16.273 | 108.0742 | 8 | 5.3078 | 2.5256 | -3.6759 | 1.9983 | -4.4505 | 8.6984 | -0.7933 | -1.0165 | 0.4056 | -0.2846 | 1.0477 | 0.7934 | 0.4592 | -1.2756 | -0.6416 | 0.1743 | -0.0358 | 0.0402 | 1.3433 | 0.4159 | 0.8229 | 44.3199 | 25.1367 | 93.4906 | 9 | 3.5097 | -1.2194 | 1.2758 | 3.5326 | -2.7886 | 6.1571 | -0.2569 | 0.9326 | 0.5036 | -0.4462 | -0.2394 | -0.711 | -0.0737 | 0.8828 | 0.3937 | 0.4526 | -0.1719 | 0.04 | 0.8129 | -0.0236 | 0.4396 | 36.0869 | 18.3724 | 106.3499 | 10 | 3.4815 | 1.6337 | -2.4523 | 2.9369 | 1.3394 | 4.6287 | -0.4666 | 0.3848 | 0.017 | -0.8695 | 0.4544 | -0.8955 | -0.2706 | 0.7561 | -0.2841 | 0.6691 | -0.1055 | 0.1091 | 1.4398 | -0.05 | 0.5257 | 36.2521 | 19.7985 | 96.7835 | 11 | 0.4557 | -0.4415 | -0.9602 | 0.6367 | 0.0717 | 5.9928 | -0.0866 | 1.1203 | -0.0899 | -0.2495 | 0.1048 | -0.6027 | -0.5415 | 0.9511 | 0.5234 | 0.4268 | -0.1974 | 0.0709 | 0.8281 | 0.0085 | 0.5279 | 39.241 | 16.8412 | 113.9626 | 12 | -0.0197 | 0.0185 | -0.0521 | 0.0595 | -0.3041 | 1.176 | -0.712 | -0.2586 | 0.2832 | -0.0327 | -0.4674 | -0.8988 | -0.71 | -1.1423 | 1.0702 | 0.5705 | -0.1377 | -0.0333 | 0.7226 | 0.1211 | 0.9603 | 45.1913 | 23.7729 | 106.9392 | 13 | 6.6787 | 2.3669 | -5.8285 | 6.9568 | -3.4104 | 7.311 | -0.3143 | -1.0672 | -0.9405 | 0.2095 | -0.3149 | -0.1875 | 0.1903 | 0.7824 | 0.5124 | 0.3735 | 0.0561 | -0.0528 | 0.5182 | 0.1468 | 0.5816 | 51.907 | -18.0684 | 158.2325 | 14 | 0.9023 | 2.0408 | -1.4589 | 8.7668 | -7.4187 | 6.4902 | -0.0976 | -0.0602 | -0.0029 | 1.0606 | -0.6944 | -0.9401 | -0.8714 | 0.8057 | 0.807 | 0.4556 | -0.039 | -0.1111 | 0.5894 | 0.1287 | 0.4824 | 48.689 | -22.5371 | 171.9013 | 15 | 2.8512 | -1.5858 | 0.3989 | 6.5843 | -3.7753 | 4.0178 | 0.1255 | -0.1942 | 0.1266 | -0.0469 | 0.0322 | -0.0885 | 0.5435 | 0.2448 | -0.1594 | 0.42 | -0.0167 | -0.1381 | 0.4794 | 0.0997 | 0.3931 | 42.3301 | -17.4849 | 158.2672 | 16 | 5.3766 | -3.9042 | 0.7984 | 7.5722 | -0.8305 | 0.4401 | 0.2476 | 0.4886 | -1.1733 | -1.1011 | 0.0913 | 0.6677 | 0.4689 | 0.1418 | -0.4834 | 0.9153 | 0.0984 | -0.0148 | 0.6941 | -0.0558 | 0.7296 | 40.8734 | -36.2153 | 161.4323 | 17 | 4.8261 | -3.6917 | 0.6761 | 8.0592 | -0.6382 | 0.1881 | 0.0888 | 0.0997 | -0.3751 | -0.3079 | 0.3493 | 0.2624 | 0.4093 | -0.1225 | -0.3442 | 0.4915 | -0.071 | 0.0143 | 0.5713 | 0.1752 | 0.4484 | 36.9803 | -21.567 | 163.3936 | 18 | 4.4801 | -3.8383 | 3.4435 | 5.8935 | -4.2765 | 5.4527 | 0.0686 | -0.9365 | -1.0978 | 0.0918 | 0.3946 | 0.8416 | 0.308 | -0.571 | -0.3734 | 0.4066 | -0.0473 | 0.0207 | 0.6875 | 0.2156 | 0.3936 | 33.056 | -19.3965 | 166.2443 | 19 | 7.1732 | -2.9049 | 0.2022 | 2.1474 | -2.7975 | 8.1443 | -0.0922 | -1.0648 | -0.4031 | 0.7134 | 0.5026 | 0.9284 | -0.2448 | -0.2639 | -0.4236 | 0.459 | 0.0266 | 0.0251 | 0.5766 | 0.0949 | 0.4381 | 38.0985 | -18.5097 | 171.4292 | 20 | 3.2747 | 1.5028 | -2.2561 | 5.9302 | 3.7282 | 6.6305 | 0.279 | -0.3619 | 0.4817 | 0.6664 | -0.2627 | -0.1215 | -0.4666 | 0.4561 | -0.2306 | 0.4655 | -0.0287 | -0.0744 | 0.5359 | 0.1067 | 0.5276 | 45.4247 | -13.4805 | 167.3615 | 21 | 2.4145 | -2.6103 | 2.5514 | 5.2428 | -5.1001 | 4.96 | -0.228 | -0.4353 | -0.3681 | 0.6166 | 0.6989 | 1.4141 | 0.4489 | -0.6951 | -0.8996 | 0.6551 | 0.0179 | 0.0186 | 0.5485 | 0.2382 | 0.6417 | 40.9723 | -30.9041 | 175.6977 | 22 | 1.6318 | -2.7342 | 3.1432 | 4.4584 | -5.2869 | 6.063 | 0.7303 | 0.2611 | -0.4199 | -0.5139 | -0.3265 | 0.1628 | 1.1445 | 0.2885 | -0.212 | 0.5105 | 0.0312 | -0.1298 | 0.4899 | 0.1006 | 0.6141 | 43.4103 | -21.2256 | 158.322 | 23 | 1.4518 | -0.527 | 0.5578 | 4.8873 | -2.0049 | 5.0763 | -0.1062 | 0.9835 | 0.4061 | -0.1751 | 0.3316 | 0.3392 | -0.4195 | -0.033 | -0.3805 | 0.2886 | -0.0146 | -0.0114 | 0.3819 | 0.1289 | 0.3856 | 38.5731 | -10.7306 | 144.1561 | 24 | 2.0951 | 1.9719 | -3.4939 | 1.7861 | -3.29 | 5.806 | -0.0618 | -0.4633 | -0.2715 | -0.0431 | -0.961 | -0.4559 | 0.86 | 1.8731 | 1.02 | 0.616 | 0.0951 | -0.0348 | 0.5885 | 0.1759 | 0.6233 | 49.0576 | -28.4078 | 167.0705 |
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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 224 through 303 )A0 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 304 through 380 )A0 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 381 through 530 )A0 | 4 | X-RAY DIFFRACTION | 4 | chain 'B' and (resid 224 through 323 )B0 | 5 | X-RAY DIFFRACTION | 5 | chain 'B' and (resid 324 through 437 )B0 | 6 | X-RAY DIFFRACTION | 6 | chain 'B' and (resid 438 through 530 )B0 | 7 | X-RAY DIFFRACTION | 7 | chain 'C' and (resid 1 through 6 )C0 | 8 | X-RAY DIFFRACTION | 8 | chain 'C' and (resid 7 through 20 )C0 | 9 | X-RAY DIFFRACTION | 9 | chain 'C' and (resid 21 through 63 )C0 | 10 | X-RAY DIFFRACTION | 10 | chain 'C' and (resid 64 through 91 )C0 | 11 | X-RAY DIFFRACTION | 11 | chain 'C' and (resid 92 through 106 )C0 | 12 | X-RAY DIFFRACTION | 12 | chain 'C' and (resid 107 through 116 )C0 | 13 | X-RAY DIFFRACTION | 13 | chain 'D' and (resid 1 through 7 )D | | | | | | | | | | | | | | | | | | | | | | | | | |
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