ソフトウェア | 名称 | バージョン | 分類 | NB |
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DENZO | | データ削減 | | SCALEPACK | | データスケーリング | | PHENIX | 1.7.1_743精密化 | | PDB_EXTRACT | 3.1 | データ抽出 | | |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.39→48.16 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.81 / σ(F): 1.34 / 位相誤差: 28.63 / 立体化学のターゲット値: ML
| Rfactor | 反射数 | %反射 |
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Rfree | 0.275 | 2000 | 2.87 % |
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Rwork | 0.213 | - | - |
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obs | 0.215 | 69760 | 98.9 % |
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溶媒の処理 | 減衰半径: 0.53 Å / VDWプローブ半径: 0.7 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 66.19 Å2 / ksol: 0.32 e/Å3 |
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原子変位パラメータ | Biso mean: 63.67 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -9.0205 Å2 | -0 Å2 | 0 Å2 |
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2- | - | -1.7386 Å2 | -0 Å2 |
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3- | - | - | 10.7591 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.39→48.16 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 9548 | 0 | 92 | 172 | 9812 |
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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_d0.014 | 9798 | X-RAY DIFFRACTION | f_angle_d1.448 | 13252 | X-RAY DIFFRACTION | f_dihedral_angle_d17.253 | 3431 | X-RAY DIFFRACTION | f_chiral_restr0.128 | 1660 | X-RAY DIFFRACTION | f_plane_restr0.005 | 1586 | | | | | |
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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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2.394-2.4538 | 0.3456 | 136 | 0.2747 | 4604 | X-RAY DIFFRACTION | 95 | 2.4538-2.5202 | 0.3791 | 140 | 0.2793 | 4757 | X-RAY DIFFRACTION | 99 | 2.5202-2.5943 | 0.3622 | 141 | 0.2728 | 4768 | X-RAY DIFFRACTION | 99 | 2.5943-2.6781 | 0.3227 | 141 | 0.2712 | 4787 | X-RAY DIFFRACTION | 99 | 2.6781-2.7738 | 0.3558 | 141 | 0.2538 | 4757 | X-RAY DIFFRACTION | 98 | 2.7738-2.8848 | 0.3411 | 141 | 0.2413 | 4779 | X-RAY DIFFRACTION | 99 | 2.8848-3.0161 | 0.3129 | 141 | 0.2267 | 4798 | X-RAY DIFFRACTION | 99 | 3.0161-3.1751 | 0.3064 | 143 | 0.22 | 4814 | X-RAY DIFFRACTION | 99 | 3.1751-3.3739 | 0.3028 | 143 | 0.228 | 4856 | X-RAY DIFFRACTION | 100 | 3.3739-3.6344 | 0.2954 | 144 | 0.218 | 4885 | X-RAY DIFFRACTION | 100 | 3.6344-4 | 0.292 | 145 | 0.2041 | 4931 | X-RAY DIFFRACTION | 100 | 4-4.5784 | 0.2588 | 146 | 0.184 | 4928 | X-RAY DIFFRACTION | 100 | 4.5784-5.7667 | 0.2421 | 145 | 0.1918 | 4948 | X-RAY DIFFRACTION | 100 | 5.7667-48.1681 | 0.1977 | 153 | 0.1988 | 5148 | X-RAY DIFFRACTION | 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 | 0.8776 | -0.0105 | -0.7141 | 0.9564 | 0.1998 | 2.138 | -0.282 | -0.0233 | -0.3475 | -0.3764 | 0.1352 | -0.2281 | 0.5813 | 0.1573 | 0.063 | 0.7089 | -0.2367 | 0.4279 | 0.4876 | -0.1795 | 0.38 | 26.7989 | 25.0106 | -10.2147 | 2 | 1.0575 | 0.7941 | 0.0071 | 3.0073 | 1.174 | 1.2307 | -0.1108 | -0.0732 | 0.2112 | -0.4644 | 0.1747 | 0.3476 | -0.1807 | 0.2342 | 0.0512 | 0.3536 | -0.0409 | -0.0134 | 0.3826 | -0.0176 | 0.2198 | 9.2206 | 18.5807 | 6.8107 | 3 | 0.2428 | 0.2355 | 0.3108 | 1.0771 | 0.5823 | 0.4891 | -0.1645 | 0.3797 | 0.0112 | -0.7869 | 0.2749 | -0.1697 | -0.3922 | 0.2174 | 0.0484 | 0.935 | -0.2203 | -0.1843 | 0.2742 | -0.2396 | -0.2204 | 13.481 | 17.7166 | -8.9864 | 4 | 2.3675 | -0.1041 | 1.5626 | 1.2045 | -0.084 | 1.7401 | -0.0137 | -0.2885 | 0.291 | -0.249 | -0.0833 | 0.5345 | -0.0783 | -0.3053 | 0.1314 | 0.2736 | -0.0424 | -0.2289 | 0.3497 | -0.1906 | 0.7589 | -6.4754 | 16.1522 | 6.9452 | 5 | 0.24 | -0.1027 | 0.1727 | 1.1208 | 0.5862 | 1.3335 | 0.0361 | 0.227 | -0.04 | -0.8448 | 0.1575 | 0.1956 | -0.1299 | 0.2397 | -0.0527 | 0.577 | -0.0702 | -0.1582 | 0.3431 | 0.0299 | 0.2673 | 9.4499 | 26.4123 | 1.312 | 6 | 2.1952 | 0.5588 | 0.2664 | 2.1788 | 2.139 | 3.1315 | -0.1597 | -0.0486 | -0.2135 | 0.0686 | 0.2437 | 1.0053 | -0.3132 | -0.7293 | -0.2943 | 0.3355 | -0.0203 | -0.0798 | 0.5627 | 0.0367 | 0.9926 | -9.0913 | 9.244 | 2.8765 | 7 | 1.3068 | 0.1472 | 0.5109 | 0.6783 | 0.2637 | 0.9269 | 0.1236 | 0.2229 | -0.21 | -0.2698 | 0.0958 | 0.2272 | -0.0648 | 0.2826 | 0.2216 | 0.8638 | -0.0704 | -0.4341 | 0.3701 | -0.0751 | 0.3595 | 1.4973 | 22.3876 | -8.854 | 8 | 0.9388 | -0.8193 | 0.625 | 1.0289 | 0.3847 | 4.0698 | 0.0941 | 0.4516 | 0.1538 | -0.3723 | 0.1673 | -0.2085 | -0.2362 | 0.0853 | 0.1295 | 1.066 | -0.2252 | 0.2695 | 0.5549 | 0.039 | 0.2439 | 20.2529 | 36.8924 | -12.583 | 9 | 2.1692 | 0.5254 | 0.5908 | 1.416 | -0.5503 | 6.3558 | -0.3543 | 0.5394 | -0.5529 | -0.6331 | 0.2988 | -0.3172 | 0.4864 | 0.4645 | 0.324 | 0.7152 | -0.1589 | 0.4197 | 0.4078 | -0.1414 | 0.5942 | 32.1276 | 51.7168 | 1.6877 | 10 | 1.2279 | -0.4892 | 0.2748 | 2.0263 | -0.2588 | 1.3072 | -0.2027 | 0.0421 | 0.0147 | -0.5432 | 0.0682 | 0.4156 | -0.2274 | -0.0262 | -0.0614 | 0.4518 | -0.0827 | -0.0417 | 0.3498 | -0.028 | 0.2457 | 9.7684 | 41.2842 | 6.389 | 11 | 1.3507 | -0.5591 | 0.0856 | 0.9443 | -0.9774 | 1.7296 | -0.0913 | 0.3745 | 0.1444 | -0.3884 | 0.3113 | -0.0842 | 0.1338 | -0.0714 | 0.0249 | 0.436 | -0.0512 | 0.2378 | 0.2938 | 0.0681 | 0.2794 | 26.683 | 57.8116 | 2.8194 | 12 | 1.0179 | 0.3673 | 0.6644 | 0.6153 | 0.263 | 1.6589 | -0.0858 | 0.2789 | 0.0662 | -0.4634 | 0.2898 | 0.1413 | -0.1155 | -0.1736 | 0.3094 | 0.7675 | 0.0371 | -0.2141 | 0.182 | 0.1468 | -0.0747 | 11.9798 | 50.703 | -4.4031 | 13 | 1.1557 | -0.2624 | -0.169 | 0.7137 | 0.4697 | 2.4016 | 0.2946 | -0.0775 | -0.2726 | -0.3197 | -0.1387 | 0.8958 | 0.3418 | -0.591 | -0.2279 | 0.2948 | 0.039 | -0.2374 | 0.5146 | 0.0702 | 0.7396 | -5.2117 | 46.2516 | 7.5789 | 14 | 0.7045 | 0.0802 | 0.4419 | 1.5384 | 0.1029 | 1.2362 | -0.0344 | 0.1129 | 0.2571 | -0.5579 | -0.0614 | 0.0763 | -0.3024 | 0.1552 | -0.0142 | 0.4448 | -0.0096 | -0.0452 | 0.3165 | -0.0313 | 0.2933 | 13.9795 | 48.4985 | 11.0705 | 15 | 5.0718 | 4.3073 | 0.0187 | 6.469 | 1.0972 | 2.0436 | 0.1662 | -0.6328 | 0.0515 | 0.1298 | -0.2967 | 1.1632 | 0.091 | -0.8089 | 0.2336 | 0.385 | 0.0158 | -0.2181 | 0.8562 | 0.1853 | 0.8501 | -8.9305 | 48.9112 | 0.8438 | 16 | 4.1922 | -1.0419 | 1.4733 | 2.4985 | -0.0861 | 2.5742 | 0.4343 | -0.1513 | -0.1593 | -0.5104 | -0.1178 | 0.1847 | -0.3664 | -0.4685 | -0.2955 | 0.5264 | 0.0397 | -0.0291 | 0.3805 | 0.1279 | 0.4524 | 8.1008 | 59.0849 | 4.9599 | 17 | 0.2724 | 0.9568 | 0.575 | 4.772 | -0.3497 | 5.1328 | 0.0495 | 0.3631 | 0.533 | 0.2021 | 0.2597 | -0.9105 | -0.293 | 0.3958 | -0.3927 | 0.4729 | -0.173 | 0.1869 | 0.3367 | -0.142 | 0.5756 | 31.1919 | 60.1341 | 12.7214 | 18 | 0.7799 | 0.126 | 0.3658 | 0.5331 | 0.4678 | 0.7536 | -0.2434 | 0.0035 | 0.3655 | 0.3759 | 0.1678 | -0.4451 | -0.2076 | 0.259 | -0.0322 | 0.5166 | -0.0639 | -0.7563 | 0.4966 | -0.1569 | 1.3176 | 44.3712 | 18.6427 | 33.8449 | 19 | 0.9944 | 0.0637 | 0.2159 | 1.2252 | 0.5718 | 0.6196 | 0.128 | -0.6512 | -0.1599 | 1.2778 | 0.1154 | -0.6198 | 0.2578 | 0.1199 | 0.4977 | 0.8032 | -0.0851 | -0.5684 | 0.3298 | 0.0693 | 0.0233 | 28.3147 | 27.0035 | 42.0599 | 20 | 1.1356 | 0.3096 | 0.0716 | 0.1903 | -0.4209 | 1.8501 | 0.097 | -0.5021 | 0.0655 | 0.3212 | -0.0162 | 0.1179 | 0.1931 | -0.2358 | -0.1572 | 1.0766 | -0.0838 | 0.2918 | 0.5716 | -0.1097 | 0.178 | 11.3737 | 29.7033 | 50.3494 | 21 | 1.0262 | -0.6784 | 0.135 | 1.0215 | -0.4113 | 0.9536 | 0.1422 | -0.4008 | -0.2731 | 0.7014 | -0.0153 | -0.479 | 0.4549 | 0.1541 | 0.028 | 0.642 | -0.0485 | -0.2315 | 0.3352 | -0.0102 | 0.2658 | 24.9862 | 18.9009 | 33.9221 | 22 | 1.832 | 0.3782 | 0.8498 | 3.96 | -0.6743 | 1.0264 | -0.022 | -0.7601 | 0.2433 | 1.0162 | -0.072 | 0.2346 | -0.4396 | -0.6511 | 0.1575 | 1.4642 | -0.1437 | -0.1832 | 0.6854 | -0.0154 | 0.2519 | 18.762 | 28.0579 | 51.5805 | 23 | 0.4247 | -0.0308 | -0.1161 | 0.8538 | -0.4085 | 1.0653 | 0.1299 | -0.1105 | -0.0691 | 0.487 | -0.1146 | -0.2812 | -0.0837 | 0.1405 | 0.0906 | 1.1172 | -0.0688 | -0.5681 | 0.346 | 0.2467 | 0.5033 | 29.1608 | 13.2959 | 44.5706 | 24 | 5.7619 | -2.7511 | 1.1223 | 1.7569 | -1.1768 | 2.3812 | 0.4436 | 0.4636 | -0.9914 | -0.2044 | -0.3805 | 0.2985 | 0.3463 | 0.2122 | -0.4295 | 0.5514 | 0.0858 | -0.3923 | 0.6346 | 0.085 | 1.334 | 45.6743 | -1.0832 | 31.1345 | 25 | 2.4969 | -0.6398 | 0.9874 | 1.0171 | -0.6762 | 2.0818 | 0.1906 | 0.2167 | 0.5987 | -0.1942 | -0.2212 | -0.353 | -0.092 | 0.3393 | 0.3587 | 0.1973 | 0.1565 | 0.0259 | 0.432 | -0.0244 | 0.8146 | 33.8523 | 4.7235 | 9.8551 | 26 | 1.2731 | -0.2278 | -0.3377 | 2.166 | 0.1004 | 2.8246 | -0.0269 | -0.1951 | -0.2672 | 0.7671 | -0.0085 | 0.0861 | 0.4803 | -0.2056 | -0.0054 | 0.2538 | -0.0424 | -0.0214 | 0.1276 | 0.0122 | 0.3172 | 17.1272 | 11.8612 | 27.0286 | 27 | 2.2408 | 0.61 | 0.3196 | 1.6191 | -1.0996 | 1.0242 | -0.321 | -0.0166 | -0.4177 | 0.0622 | 0.0501 | -0.3128 | 0.0936 | 0.0655 | -0.0724 | 0.2462 | -0.0542 | 0.0731 | 0.419 | -0.0323 | 0.5697 | 27.5588 | -0.5225 | 9.3563 | 28 | 1.4084 | 0.3673 | -0.4188 | 2.4682 | -0.6607 | 3.3429 | 0.1133 | -0.259 | -0.2413 | 0.6816 | 0.0811 | -0.2626 | -0.0562 | -0.0102 | 0.3205 | 0.382 | -0.0579 | -0.1527 | 0.1195 | 0.1326 | 0.3071 | 22.8928 | -1.3947 | 26.7648 | 29 | 0.7836 | 0.5273 | -0.0333 | 1.8663 | -0.1862 | 0.9598 | 0.3608 | -0.2591 | 0.0837 | 0.8506 | -0.1773 | 0.4484 | -0.3464 | -0.0238 | 0.1967 | 0.7891 | -0.1172 | 0.3872 | 0.2177 | 0.0047 | 0.6212 | 3.9585 | 5.9711 | 33.3869 | 30 | 1.2437 | -0.1123 | 0.2565 | 3.0383 | 0.2364 | 1.7647 | 0.476 | 0.0905 | 0.0743 | 0.1268 | -0.0932 | -0.2099 | 0.2249 | 0.3332 | -0.1452 | 0.2974 | 0.0044 | 0.0461 | 0.2767 | 0.0012 | 0.3315 | 14.4035 | 5.7572 | 12.8483 | 31 | 1.2581 | -0.0532 | 1.1779 | 3.6624 | 0.6439 | 2.094 | -0.0372 | 0.1241 | 0.2945 | 0.0595 | 0.1279 | -0.6871 | 0.18 | 0.2884 | -0.1302 | 0.2475 | 0.0178 | 0.0279 | 0.3248 | -0.0427 | 0.2417 | 19.3929 | 18.1136 | 15.5753 | 32 | 1.7483 | -0.2334 | -0.1257 | 1.8327 | 0.5026 | 0.5742 | -0.1373 | -0.2897 | -0.2343 | 0.9696 | -0.0044 | 0.0682 | 0.2164 | -0.0779 | -0.1851 | 0.6417 | -0.078 | -0.099 | 0.3493 | -0.1029 | 0.3434 | 11.9982 | 2.751 | 27.8135 | 33 | 2.8861 | 0.4374 | 0.275 | 1.1194 | 1.2134 | 3.7722 | 0.4512 | -0.6049 | 0.2105 | 0.7125 | -0.4909 | 0.4002 | -1.1211 | -1.0856 | 0.0298 | 0.921 | -0.1277 | 0.4541 | 0.8379 | -0.0953 | 0.6142 | 4.2948 | -1.021 | 38.5281 | 34 | 3.8004 | 1.6642 | -3.4568 | 3.0497 | -3.9187 | 9.1541 | -0.1558 | -0.0848 | -0.4656 | 0.294 | -0.0387 | -0.001 | -0.7512 | -0.0888 | 0.1427 | 0.3166 | 0.0054 | 0.14 | 0.2545 | -0.0822 | 0.5599 | 12.398 | -3.4575 | 18.7228 | 35 | 5.2638 | 0.9113 | 0.196 | 5.5336 | -2.8225 | 6.7421 | -0.2049 | 0.6461 | -0.3065 | -0.7834 | 0.0025 | -1.0943 | -0.1381 | 0.6473 | 0.2196 | 0.467 | -0.0836 | 0.149 | 0.4408 | -0.0911 | 0.5581 | 25.1261 | 4.2869 | -0.4437 | 36 | 0.3443 | 0.3494 | 0.547 | 2.8261 | -0.0841 | 1.4141 | 0.0125 | -0.1532 | 0.189 | 0.5477 | 0.0505 | -0.6289 | -0.2278 | 0.2229 | 0.0862 | 0.2737 | -0.0253 | -0.0544 | 0.2186 | -0.1219 | 0.4051 | 24.8614 | 48.7342 | 27.6812 | 37 | 0.3433 | 0.2824 | -0.3642 | 0.6209 | -0.0148 | 0.5438 | 0.1294 | -0.1715 | -0.0023 | 0.535 | 0.031 | -0.6852 | -0.0718 | 0.0921 | 0.148 | 0.3596 | 0.0103 | -0.1785 | 0.2525 | -0.1119 | 0.5474 | 30.1576 | 54.6053 | 30.2324 | 38 | 1.7399 | 0.3618 | 1.1091 | 2.4854 | 0.2864 | 5.8457 | 0.3194 | -0.4136 | 0.0979 | 0.3454 | -0.0683 | 0.622 | 0.0473 | -0.4244 | 0.0617 | 0.3828 | -0.0049 | 0.1589 | 0.3959 | -0.183 | 0.515 | 5.7182 | 54.632 | 34.4138 | 39 | 0.2403 | 0.4655 | 0.3775 | 1.0732 | 0.4589 | 0.8563 | 0.2045 | -0.0785 | -0.0523 | 0.582 | -0.2001 | -0.6027 | 0.089 | 0.1818 | -0.227 | 0.4289 | -0.0552 | -0.1113 | 0.3481 | -0.0672 | 0.2798 | 22.8587 | 45.0755 | 33.7678 | 40 | 3.3975 | -1.0201 | -0.7542 | 1.3938 | -0.2572 | 1.2548 | 0.2971 | -0.018 | -0.0698 | -0.1566 | -0.2775 | 0.3676 | -0.42 | -0.8424 | 0.1286 | 0.6663 | 0.1386 | 0.2657 | 0.9927 | -0.3789 | 1.1019 | 4.5683 | 62.7917 | 35.5089 | 41 | 2.6928 | -1.1305 | -0.432 | 1.9616 | -0.0175 | 1.6856 | 0.2682 | -0.2221 | 0.0348 | 0.2843 | 0.2548 | -0.288 | -0.2468 | 0.341 | -0.0987 | 0.8655 | -0.141 | -0.0848 | 0.416 | -0.0907 | 0.3035 | 22.7214 | 55.8745 | 41.9827 | 42 | 0.8616 | 0.3399 | 0.1673 | 1.5721 | 0.6651 | 0.9657 | 0.102 | 0.0412 | -0.1173 | 0.1801 | 0.1472 | -0.4557 | 0.3204 | 0.1947 | 0.2397 | 0.4935 | 0.0769 | -0.5783 | 0.3112 | -0.1034 | 0.8178 | 41.9691 | 40.9151 | 40.9432 |
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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 (resseq 0:23)2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resseq 24:82)3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resseq 83:129)4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resseq 130:152)5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resseq 153:214)6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resseq 215:222)7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resseq 223:242)8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resseq 243:256)9 | X-RAY DIFFRACTION | 9 | chain 'B' and (resseq 0:23)10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resseq 24:82)11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resseq 83:100)12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resseq 101:129)13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resseq 130:152)14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resseq 153:214)15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resseq 215:222)16 | X-RAY DIFFRACTION | 16 | chain 'B' and (resseq 223:242)17 | X-RAY DIFFRACTION | 17 | chain 'B' and (resseq 243:256)18 | X-RAY DIFFRACTION | 18 | chain 'C' and ( | | | | | | | | | | | | | | | | | |
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