Software | Name | Version | Classification |
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PHENIX | dev_5533refinementAimless | | data scalingXDS | | data reductionPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.25 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1974 | 6864 | 5.02 % |
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Rwork | 0.1637 | - | - |
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obs | 0.1654 | 136822 | 99.82 % |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Refinement step | Cycle: LAST / Resolution: 1.8→48.25 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 10701 | 0 | 42 | 855 | 11598 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 11034 | X-RAY DIFFRACTION | f_angle_d0.999 | 14998 | X-RAY DIFFRACTION | f_dihedral_angle_d13.512 | 4011 | X-RAY DIFFRACTION | f_chiral_restr0.058 | 1749 | X-RAY DIFFRACTION | f_plane_restr0.012 | 1937 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.8-1.82 | 0.2743 | 214 | 0.239 | 4262 | X-RAY DIFFRACTION | 100 | 1.82-1.84 | 0.2645 | 223 | 0.2458 | 4290 | X-RAY DIFFRACTION | 100 | 1.84-1.86 | 0.2443 | 225 | 0.2254 | 4384 | X-RAY DIFFRACTION | 100 | 1.86-1.89 | 0.2575 | 222 | 0.214 | 4266 | X-RAY DIFFRACTION | 100 | 1.89-1.91 | 0.2623 | 230 | 0.2072 | 4259 | X-RAY DIFFRACTION | 100 | 1.91-1.94 | 0.2712 | 211 | 0.2089 | 4409 | X-RAY DIFFRACTION | 100 | 1.94-1.97 | 0.3002 | 225 | 0.2102 | 4246 | X-RAY DIFFRACTION | 100 | 1.97-2 | 0.2689 | 230 | 0.2108 | 4323 | X-RAY DIFFRACTION | 100 | 2-2.03 | 0.2198 | 235 | 0.1855 | 4314 | X-RAY DIFFRACTION | 100 | 2.03-2.06 | 0.2292 | 236 | 0.1687 | 4255 | X-RAY DIFFRACTION | 100 | 2.06-2.1 | 0.2049 | 215 | 0.1609 | 4350 | X-RAY DIFFRACTION | 100 | 2.1-2.13 | 0.2204 | 239 | 0.1611 | 4251 | X-RAY DIFFRACTION | 100 | 2.13-2.18 | 0.1842 | 231 | 0.1575 | 4394 | X-RAY DIFFRACTION | 100 | 2.18-2.22 | 0.2262 | 236 | 0.1565 | 4266 | X-RAY DIFFRACTION | 100 | 2.22-2.27 | 0.2055 | 234 | 0.159 | 4321 | X-RAY DIFFRACTION | 100 | 2.27-2.32 | 0.2119 | 220 | 0.1585 | 4289 | X-RAY DIFFRACTION | 100 | 2.32-2.38 | 0.1868 | 210 | 0.1544 | 4369 | X-RAY DIFFRACTION | 100 | 2.38-2.44 | 0.1952 | 235 | 0.1499 | 4316 | X-RAY DIFFRACTION | 100 | 2.44-2.51 | 0.2009 | 204 | 0.1597 | 4375 | X-RAY DIFFRACTION | 100 | 2.51-2.6 | 0.2068 | 257 | 0.1642 | 4269 | X-RAY DIFFRACTION | 100 | 2.6-2.69 | 0.1884 | 210 | 0.1556 | 4363 | X-RAY DIFFRACTION | 100 | 2.69-2.8 | 0.2041 | 203 | 0.1607 | 4381 | X-RAY DIFFRACTION | 100 | 2.8-2.92 | 0.2003 | 241 | 0.1662 | 4327 | X-RAY DIFFRACTION | 100 | 2.92-3.08 | 0.175 | 217 | 0.1708 | 4333 | X-RAY DIFFRACTION | 100 | 3.08-3.27 | 0.2171 | 247 | 0.1691 | 4339 | X-RAY DIFFRACTION | 100 | 3.27-3.52 | 0.1894 | 252 | 0.1606 | 4336 | X-RAY DIFFRACTION | 100 | 3.52-3.88 | 0.1878 | 247 | 0.1529 | 4369 | X-RAY DIFFRACTION | 99 | 3.88-4.44 | 0.1417 | 248 | 0.1319 | 4321 | X-RAY DIFFRACTION | 99 | 4.44-5.59 | 0.1656 | 253 | 0.1362 | 4422 | X-RAY DIFFRACTION | 100 | 5.59-48.25 | 0.203 | 214 | 0.1834 | 4559 | X-RAY DIFFRACTION | 99 |
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Refinement TLS params. | Method: 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 | 0.7318 | 0.5808 | 0.9533 | 2.5748 | 1.8367 | 1.7893 | 0.1083 | -0.2357 | 0.5497 | 0.2819 | -0.166 | 0.0254 | -0.5665 | 0.2979 | 0.0702 | 0.4541 | -0.1468 | -0.015 | 0.2637 | -0.0316 | 0.2847 | -26.2113 | 41.4697 | 71.8362 | 2 | 4.7516 | 1.0364 | -0.7441 | 1.6897 | -0.3458 | 4.3262 | 0.0902 | -0.3467 | -0.1741 | 0.2872 | -0.1773 | -0.2663 | -0.1256 | 0.7574 | 0.0874 | 0.2867 | -0.0492 | -0.0428 | 0.3208 | -0.0173 | 0.1975 | -19.6563 | 26.0716 | 73.7581 | 3 | 0.7605 | 0.2853 | -0.4061 | 1.0103 | 0.2789 | 0.5746 | 0.125 | -0.2882 | 0.1308 | 0.1407 | -0.0617 | -0.1215 | -0.2509 | 0.388 | -0.0197 | 0.3049 | -0.1364 | -0.0234 | 0.321 | -0.0354 | 0.2217 | -23.0319 | 33.0758 | 70.6989 | 4 | 1.4279 | 0.0759 | -0.4364 | 5.7228 | 1.2568 | 2.5442 | 0.0409 | -0.1031 | -0.0848 | -0.1098 | -0.1494 | -0.0775 | 0.0444 | 0.4344 | 0.0853 | 0.1898 | -0.0354 | -0.0328 | 0.2878 | 0.0433 | 0.1937 | -20.823 | 20.8712 | 60.9945 | 5 | 1.9765 | -0.709 | 0.5237 | 1.3174 | -0.4588 | 2.3089 | 0.0703 | -0.048 | 0.0092 | 0.0624 | -0.0666 | -0.0079 | -0.0256 | 0.0993 | 0.0036 | 0.2017 | -0.0478 | -0.0173 | 0.1512 | -0.0173 | 0.1978 | -30.4342 | 26.5929 | 50.729 | 6 | 8.8335 | -6.5156 | 6.5512 | 6.9194 | -4.2153 | 8.7702 | 0.0273 | 0.3229 | 0.3248 | -0.0643 | -0.3063 | -0.873 | -0.0958 | 0.827 | 0.2485 | 0.176 | -0.0739 | -0.0067 | 0.473 | 0.0252 | 0.3033 | -9.5011 | 24.8496 | 55.7587 | 7 | 1.7804 | -0.2647 | -0.5561 | 1.348 | -0.1654 | 2.1061 | -0.1188 | 0.1241 | -0.0679 | 0.0322 | 0.039 | -0.0134 | 0.2948 | 0.1631 | 0.0616 | 0.2245 | 0.0235 | -0.0258 | 0.1274 | -0.0007 | 0.173 | -26.9363 | 14.7498 | 57.8639 | 8 | 1.8932 | -0.098 | -0.0395 | 0.9173 | 0.335 | 2.7174 | 0.0311 | -0.1105 | -0.226 | 0.1276 | -0.0438 | -0.0773 | 0.2477 | 0.2696 | 0.0118 | 0.1877 | -0.0203 | -0.0157 | 0.1702 | 0.0224 | 0.1863 | -25.6293 | 17.9646 | 56.9385 | 9 | 3.9035 | 2.3979 | -0.6966 | 8.7715 | -1.6698 | 4.4394 | 0.0188 | -0.379 | -0.0642 | 0.4791 | 0.1067 | -0.3816 | 0.053 | 0.5993 | -0.0861 | 0.2786 | -0.0364 | -0.0844 | 0.4877 | 0.0244 | 0.2572 | -12.6481 | 19.9312 | 67.8329 | 10 | 3.3393 | -0.2336 | -1.952 | 0.0825 | -0.0691 | 3.2467 | -0.0084 | -0.3305 | -0.1065 | 0.1177 | -0.0315 | 0.0049 | -0.0464 | 0.3215 | 0.0302 | 0.2732 | -0.0342 | -0.0195 | 0.1383 | 0.0173 | 0.2087 | -41.816 | 21.1297 | 83.2393 | 11 | 0.6129 | 0.0212 | -0.3355 | 0.0645 | -0.0712 | 1.3695 | 0.0445 | 0.0402 | -0.0068 | 0.0843 | -0.0304 | 0.0162 | -0.15 | -0.0764 | -0.0065 | 0.2673 | -0.0205 | 0.0152 | 0.1082 | 0.0046 | 0.2188 | -48.6537 | 24.3692 | 67.8052 | 12 | 3.6658 | -3.0934 | -1.7708 | 3.3358 | 0.6493 | 3.5251 | -0.0179 | 0.1119 | -0.3516 | 0.2164 | -0.1574 | 0.3383 | 0.5144 | -0.4256 | 0.0597 | 0.2567 | -0.0407 | 0.0285 | 0.1597 | -0.0236 | 0.2142 | -63.0142 | 27.2827 | 76.8783 | 13 | 1.7651 | -0.0636 | -0.8961 | 0.3162 | 0.4212 | 2.4786 | 0.106 | 0.1061 | 0.1628 | 0.1059 | 0.0001 | 0.026 | -0.4004 | -0.0216 | -0.1419 | 0.308 | 0.0141 | 0.0055 | 0.0672 | 0.0157 | 0.2262 | -48.8271 | 36.0283 | 63.5594 | 14 | 0.4646 | -0.3586 | -0.4021 | 1.0999 | 0.7652 | 0.6231 | 0.1257 | 0.0491 | 0.1058 | 0.1504 | -0.0481 | -0.0077 | -0.3061 | -0.0622 | -0.0128 | 0.3627 | -0.0078 | 0.0331 | 0.1354 | -0 | 0.2574 | -50.6899 | 32.6557 | 65.2208 | 15 | 4.1291 | 4.0426 | -0.4879 | 8.4816 | -1.6234 | 1.7917 | 0.0971 | -0.148 | 0.1826 | 0.1811 | -0.0422 | -0.237 | -0.2947 | 0.1691 | -0.0291 | 0.3114 | -0.0223 | 0.0404 | 0.1446 | -0.0392 | 0.2032 | -52.976 | 33.8068 | 82.014 | 16 | 3.0866 | -0.988 | 0.5161 | 1.1116 | -0.2491 | 1.7236 | 0.115 | 0.4416 | -0.1905 | -0.0814 | -0.1366 | -0.1767 | 0.2909 | 0.8069 | 0.0108 | 0.2366 | 0.0957 | 0.0087 | 0.4527 | -0.0114 | 0.2373 | -12.7625 | 16.3894 | 22.7339 | 17 | 2.2462 | -0.0106 | -0.159 | 1.0318 | -0.1242 | 1.9459 | 0.0168 | 0.0603 | 0.0287 | 0.1102 | -0.054 | -0.1728 | 0.0217 | 0.4744 | 0.0207 | 0.1477 | 0.0054 | -0.0115 | 0.224 | 0.0195 | 0.1425 | -18.7644 | 22.4273 | 32.084 | 18 | 1.3474 | 0.1191 | -0.4258 | 0.6557 | -0.2097 | 1.8438 | 0.0334 | -0.031 | 0.0803 | -0.01 | -0.0389 | -0.1139 | -0.1442 | 0.3409 | 0.0008 | 0.1888 | -0.0522 | -0.0213 | 0.1758 | 0.006 | 0.2053 | -23.8448 | 28.9679 | 40.5381 | 19 | 2.169 | 0.6454 | -0.5163 | 2.5365 | -0.4357 | 2.7786 | 0.0587 | 0.0533 | 0.2823 | -0.0134 | -0.0606 | -0.0215 | -0.2362 | 0.3085 | -0.0054 | 0.1812 | -0.0249 | -0.0243 | 0.238 | 0.0107 | 0.2397 | -20.9529 | 28.4066 | 35.783 | 20 | 3.7278 | -2.4439 | 0.8296 | 3.2271 | -3.421 | 5.4806 | 0.0989 | 0.3142 | 0.3873 | -0.1742 | -0.234 | -0.5163 | -0.229 | 0.6896 | 0.1624 | 0.279 | -0.071 | -0.0104 | 0.5419 | 0.0484 | 0.3753 | -7.9318 | 30.6348 | 30.732 | 21 | 2.2423 | -0.2521 | 0.6325 | 1.3411 | -0.1963 | 4.2076 | 0.0306 | 0.3018 | 0.1177 | -0.0921 | -0.0864 | -0.0306 | -0.1397 | 0.2934 | 0.0524 | 0.2213 | 0.0101 | 0.0102 | 0.2442 | 0.0353 | 0.2064 | -30.3659 | 26.7254 | 7.6936 | 22 | 1.1794 | 0.0155 | -0.1523 | 0.7627 | 0.1323 | 2.6037 | 0.0811 | 0.1162 | 0.0575 | -0.0811 | -0.0914 | 0.127 | 0.0644 | -0.112 | -0.012 | 0.1797 | 0.0161 | -0.0174 | 0.1502 | -0.0017 | 0.1692 | -38.56 | 22.493 | 16.0096 | 23 | 0.6055 | -0.2057 | -0.4469 | 1.5496 | 1.7324 | 5.8576 | 0.0553 | 0.0664 | -0.0923 | -0.0246 | -0.1451 | 0.0514 | -0.036 | -0.5165 | 0.1025 | 0.1655 | -0.0028 | -0.026 | 0.201 | -0.0126 | 0.2041 | -48.4516 | 23.0382 | 21.3895 | 24 | 0.7447 | -0.3478 | -0.2455 | 0.3087 | -0.5148 | 2.5887 | -0.0042 | -0.0307 | -0.1813 | -0.0184 | -0.0845 | 0.0566 | 0.4885 | -0.2586 | 0.0694 | 0.2898 | -0.0605 | -0.0051 | 0.1661 | -0.0344 | 0.246 | -44.0725 | 11.2249 | 25.1134 | 25 | 0.9153 | -0.4567 | -0.0947 | 4.1348 | 0.1474 | 1.934 | 0.1001 | 0.0949 | -0.1024 | 0.0996 | -0.18 | 0.0155 | 0.3493 | -0.134 | 0.0502 | 0.2262 | -0.0161 | -0.0229 | 0.1764 | -0.0218 | 0.2009 | -42.2905 | 17.1655 | 19.3908 | 26 | 3.1429 | -1.9077 | 1.0436 | 2.3537 | -2.9716 | 5.2487 | 0.169 | 0.222 | -0.0095 | -0.4413 | -0.2201 | -0.265 | 0.4266 | 0.0409 | 0.0349 | 0.2434 | 0.0109 | -0.0277 | 0.238 | -0.0526 | 0.2138 | -40.9082 | 13.7083 | 5.4997 | 27 | 2.4666 | -0.5432 | 0.8655 | 1.0803 | -0.1321 | 0.3079 | 0.0544 | 0.2675 | 0.269 | -0.0394 | -0.045 | 0.3755 | -0.2675 | -0.2324 | -0.0426 | 0.3797 | 0.2592 | 0.0697 | 0.8702 | 0.1626 | 0.4888 | -79.9542 | 37.7602 | 45.1424 | 28 | 0.2601 | -0.0983 | 0.0326 | 0.56 | 0.0915 | 0.0265 | -0.0695 | -0.1414 | -0.0915 | 0.1019 | 0.1101 | 0.3959 | 0.0187 | -0.5361 | 0.0127 | 0.2362 | -0.0407 | 0.0062 | 0.9395 | 0.0821 | 0.4102 | -83.1202 | 22.5148 | 51.2693 | 29 | 0.0046 | -0.0092 | -0.0001 | 0.3467 | 0.0141 | 0.0026 | -0.0752 | 0.3245 | 0.2057 | 0.0899 | 0.1973 | 0.2769 | -0.2778 | -0.9209 | -0.0585 | 0.2564 | 0.1392 | 0.0448 | 0.8947 | 0.0795 | 0.4331 | -79.6878 | 29.8573 | 49.1956 | 30 | 1.4312 | -0.8755 | -0.6229 | 1.4714 | 0.6805 | 1.7114 | -0.1374 | 0.0932 | -0.1581 | 0.0601 | 0.1259 | 0.1136 | 0.215 | -0.7121 | 0.0103 | 0.2164 | -0.0724 | 0.0258 | 0.4463 | 0.0048 | 0.293 | -70.8963 | 19.1666 | 56.9879 | 31 | 2.7966 | 0.414 | -1.3895 | 1.5218 | -0.4287 | 4.1084 | 0.0464 | 0.2103 | 0.0557 | -0.0074 | 0.0507 | 0.0219 | -0.13 | -0.4105 | -0.1102 | 0.2005 | 0.0344 | 0.0003 | 0.207 | 0.0005 | 0.1682 | -58.0292 | 26.0583 | 53.288 | 32 | 8.8895 | 5.5949 | -3.7108 | 6.3201 | -3.3384 | 5.5525 | 0.2009 | -0.032 | 0.2935 | 0.4689 | -0.0531 | 0.4299 | -0.2718 | -0.6465 | -0.1201 | 0.234 | 0.0481 | 0.0556 | 0.4389 | 0.013 | 0.2725 | -72.4939 | 24.2866 | 68.7313 | 33 | 1.4855 | 0.2284 | -0.2037 | 1.4329 | -0.3757 | 1.5492 | -0.0196 | 0.1323 | -0.247 | -0.0513 | 0.094 | 0.0791 | 0.3241 | -0.441 | 0.0132 | 0.243 | -0.0924 | 0.006 | 0.2721 | -0.0122 | 0.2676 | -62.1943 | 13.0394 | 54.391 | 34 | 1.4449 | -0.1822 | -0.15 | 2.9486 | -0.2653 | 1.5311 | -0.0513 | 0.2342 | -0.2179 | -0.0687 | -0.0179 | 0.4083 | 0.2745 | -0.6944 | 0.0301 | 0.2752 | -0.0571 | 0.052 | 0.3462 | -0.0077 | 0.2687 | -67.7484 | 19.2083 | 54.9603 | 35 | 2.7342 | 0.7759 | 0.0203 | 7.1132 | 0.7571 | 2.5556 | -0.0775 | 0.181 | -0.3326 | -0.0105 | 0.1993 | 0.3995 | 0.1636 | -0.8899 | -0.0721 | 0.2516 | -0.0803 | 0.0475 | 0.776 | 0.021 | 0.403 | -80.7291 | 17.3625 | 60.7931 | 36 | 0.5607 | 0.3494 | -0.0974 | 0.3303 | 0.1998 | 0.6195 | -0.069 | 0.3307 | -0.0922 | -0.1149 | 0.01 | 0.3364 | 0.1366 | -0.6918 | -0.4149 | 0.1404 | -0.2521 | -0.0518 | 1.2496 | 0.0367 | 0.4031 | -78.2134 | 16.2103 | 28.9579 | 37 | 1.0911 | 0.0457 | 0.0453 | 0.334 | 0.0123 | 0.592 | -0.0325 | 0.3827 | -0.0746 | -0.1051 | 0.0821 | 0.2079 | 0.1581 | -1.0068 | -0.019 | 0.217 | -0.1341 | -0.0366 | 0.7933 | -0.0098 | 0.2903 | -67.245 | 19.8264 | 28.7173 | 38 | 1.3066 | -0.3754 | 1.0572 | 1.2306 | -0.7162 | 2.3054 | 0.0177 | 0.5409 | 0.1373 | -0.0845 | 0.1184 | 0.1511 | -0.1615 | -0.6364 | 0.065 | 0.1759 | 0.0009 | -0.0106 | 0.618 | 0.072 | 0.2728 | -62.2181 | 29.1437 | 23.3366 | 39 | 1.9359 | 0.0656 | 0.1852 | 0.2729 | -0.4118 | 1.8773 | -0.0561 | 0.2662 | 0.2051 | -0.0566 | 0.0976 | 0.3299 | -0.1452 | -0.782 | -0.0094 | 0.2427 | 0.0345 | -0.0163 | 0.4852 | 0.0058 | 0.2408 | -60.9359 | 29.3542 | 27.8257 | 40 | 1.7367 | 0.1232 | 0.3647 | 4.6724 | -0.2249 | 1.7945 | -0.2072 | 0.0615 | 0.2838 | 0.1189 | 0.5207 | 0.4245 | -0.1049 | -0.9267 | -0.244 | 0.3085 | -0.0052 | -0.0184 | 1.1436 | 0.0462 | 0.4575 | -74.6805 | 28.2957 | 17.523 |
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Refinement TLS group | ID | Refine-ID | Refine TLS-ID | Selection details |
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1 | X-RAY DIFFRACTION | 1 | chain 'A' and (resid 1 through 15 )2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 16 through 33 )3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 34 through 79 )4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 80 through 103 )5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 104 through 131 )6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 132 through 144 )7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 145 through 166 )8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 167 through 214 )9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 215 through 236 )10 | X-RAY DIFFRACTION | 10 | chain 'B' and (resid 1 through 55 )11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 56 through 131 )12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 132 through 145 )13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 146 through 166 )14 | X-RAY DIFFRACTION | 14 | chain 'B' and (resid 167 through 214 )15 | X-RAY DIFFRACTION | 15 | chain 'B' and (resid 215 through 236 )16 | X-RAY DIFFRACTION | 16 | chain 'C' | | | | | | | | | | | | | | | |
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