Software | Name | Version | Classification |
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XDS | | data scalingPHENIX | (phenix.refine)refinementXDS | | data reduction | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MD83md8 PDB Unreleased entry Resolution: 1.5→29.125 Å / SU ML: 0.17 / σ(F): 1.8 / Stereochemistry target values: ML
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1812 | 5289 | 7.05 % | Random |
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Rwork | 0.1521 | - | - | - |
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obs | 0.1541 | 75064 | 99.2 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.718 Å2 / ksol: 0.38 e/Å3 |
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Displacement parameters | | Baniso -1 | Baniso -2 | Baniso -3 |
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1- | 0.757 Å2 | -0 Å2 | 0.567 Å2 |
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2- | - | -1.166 Å2 | -0 Å2 |
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3- | - | - | 0.408 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.5→29.125 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 3730 | 0 | 18 | 537 | 4285 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.009 | 3791 | X-RAY DIFFRACTION | f_angle_d1.195 | 5145 | X-RAY DIFFRACTION | f_dihedral_angle_d14.651 | 1412 | X-RAY DIFFRACTION | f_chiral_restr0.073 | 622 | X-RAY DIFFRACTION | f_plane_restr0.005 | 668 | | | | | |
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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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1.5-1.517 | 0.2177 | 208 | 0.1809 | 2313 | X-RAY DIFFRACTION | 100 | 1.517-1.5349 | 0.2035 | 186 | 0.1694 | 2271 | X-RAY DIFFRACTION | 99 | 1.5349-1.5536 | 0.2261 | 187 | 0.1675 | 2306 | X-RAY DIFFRACTION | 100 | 1.5536-1.5733 | 0.19 | 206 | 0.1645 | 2322 | X-RAY DIFFRACTION | 99 | 1.5733-1.594 | 0.1961 | 163 | 0.155 | 2327 | X-RAY DIFFRACTION | 99 | 1.594-1.6158 | 0.1873 | 164 | 0.1506 | 2308 | X-RAY DIFFRACTION | 99 | 1.6158-1.6389 | 0.1815 | 173 | 0.1511 | 2339 | X-RAY DIFFRACTION | 99 | 1.6389-1.6633 | 0.1739 | 173 | 0.1473 | 2315 | X-RAY DIFFRACTION | 99 | 1.6633-1.6893 | 0.1903 | 191 | 0.1457 | 2301 | X-RAY DIFFRACTION | 99 | 1.6893-1.717 | 0.1818 | 163 | 0.1514 | 2349 | X-RAY DIFFRACTION | 99 | 1.717-1.7466 | 0.1815 | 188 | 0.1414 | 2279 | X-RAY DIFFRACTION | 99 | 1.7466-1.7784 | 0.1822 | 195 | 0.143 | 2273 | X-RAY DIFFRACTION | 98 | 1.7784-1.8126 | 0.1832 | 185 | 0.1479 | 2300 | X-RAY DIFFRACTION | 99 | 1.8126-1.8496 | 0.1766 | 186 | 0.1434 | 2246 | X-RAY DIFFRACTION | 98 | 1.8496-1.8898 | 0.1681 | 153 | 0.1396 | 2374 | X-RAY DIFFRACTION | 99 | 1.8898-1.9337 | 0.1726 | 179 | 0.1333 | 2352 | X-RAY DIFFRACTION | 100 | 1.9337-1.9821 | 0.1583 | 157 | 0.1385 | 2337 | X-RAY DIFFRACTION | 100 | 1.9821-2.0357 | 0.1352 | 191 | 0.1377 | 2322 | X-RAY DIFFRACTION | 100 | 2.0357-2.0956 | 0.1546 | 190 | 0.1277 | 2317 | X-RAY DIFFRACTION | 100 | 2.0956-2.1632 | 0.1527 | 174 | 0.1355 | 2357 | X-RAY DIFFRACTION | 100 | 2.1632-2.2405 | 0.1584 | 148 | 0.1335 | 2338 | X-RAY DIFFRACTION | 99 | 2.2405-2.3301 | 0.1845 | 192 | 0.1384 | 2318 | X-RAY DIFFRACTION | 99 | 2.3301-2.4361 | 0.1881 | 140 | 0.1513 | 2348 | X-RAY DIFFRACTION | 99 | 2.4361-2.5645 | 0.1798 | 153 | 0.1537 | 2329 | X-RAY DIFFRACTION | 98 | 2.5645-2.7251 | 0.1925 | 159 | 0.1573 | 2303 | X-RAY DIFFRACTION | 98 | 2.7251-2.9353 | 0.1806 | 182 | 0.1565 | 2369 | X-RAY DIFFRACTION | 100 | 2.9353-3.2303 | 0.1738 | 173 | 0.1558 | 2342 | X-RAY DIFFRACTION | 100 | 3.2303-3.697 | 0.167 | 176 | 0.1432 | 2365 | X-RAY DIFFRACTION | 100 | 3.697-4.6547 | 0.1682 | 153 | 0.1435 | 2371 | X-RAY DIFFRACTION | 99 | 4.6547-29.1305 | 0.21 | 201 | 0.1845 | 2384 | 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 | 0.0225 | -0.0357 | 0.0516 | 0.0441 | -0.0097 | 0.0324 | 0.1724 | -0.1858 | -0.2248 | 0.0688 | -0.0698 | 0.2812 | 0.1363 | 0.07 | -0 | 0.1175 | -0.0271 | -0.0407 | 0.148 | 0.004 | 0.2309 | -32.0673 | -19.6372 | -14.2192 | 2 | 0.2482 | -0.4102 | 0.2372 | 0.2599 | -0.1026 | 0.172 | 0.0274 | -0.0131 | -0.0731 | -0.0582 | -0.0289 | 0.0426 | 0.0651 | 0.0761 | -0 | 0.1249 | -0.0094 | -0.0105 | 0.1245 | -0.0042 | 0.139 | -24.1668 | -22.4689 | -13.1353 | 3 | 0.0159 | 0.0033 | 0.0042 | 0.0028 | 0.0329 | 0.0271 | -0.1311 | 0.1857 | -0.2965 | -0.4422 | -0.3157 | -0.5789 | 0.1945 | 0.2807 | -0 | 0.2874 | 0.0476 | 0.0376 | 0.2193 | -0.0591 | 0.3033 | -18.342 | -26.0539 | -18.3275 | 4 | 0.0536 | 0.1199 | -0.023 | 0.0784 | 0.0804 | -0.0798 | 0.181 | 0.4347 | -0.0004 | -0.152 | -0.1038 | -0.4577 | 0.1198 | 0.4011 | -0 | 0.2316 | 0.0391 | -0.0244 | 0.254 | 0.017 | 0.1882 | -22.1527 | -13.3643 | -20.3336 | 5 | 0.2308 | -0.0786 | -0.1068 | 0.2373 | 0.1719 | 0.2782 | 0.1148 | 0.0272 | 0.0418 | -0.2358 | 0.1332 | 0.3089 | 0.0829 | -0.4042 | 0.0259 | 0.1553 | 0.0123 | -0.0624 | 0.2142 | 0.0334 | 0.1628 | -33.8045 | -13.4685 | -19.2627 | 6 | 0.0848 | -0.0945 | 0.0882 | 0.043 | -0.3275 | 0.1894 | -0.0951 | -0.2678 | 0.1049 | 0.073 | 0.0519 | -0.0325 | -0.1374 | -0.0689 | -0 | 0.1255 | 0.0264 | -0.0304 | 0.1435 | 0.0104 | 0.1579 | -29.2313 | -8.0833 | -11.2796 | 7 | 0.0053 | -0.139 | -0.1466 | 0.6038 | -0.2845 | 0.1934 | 0.048 | -0.2998 | 0.081 | 0.0794 | -0.053 | -0.2271 | -0.1483 | 0.0152 | -0 | 0.0906 | -0.0062 | 0.0022 | 0.1374 | 0.0109 | 0.1157 | -20.4241 | -16.7792 | -0.3988 | 8 | 0.0263 | -0.0052 | -0.0123 | -0.0029 | -0.0163 | 0.0301 | 0.0529 | -0.4407 | -0.6607 | 0.0273 | 0.2416 | 0.2275 | 0.2579 | -0.5132 | 0 | 0.1555 | -0.0665 | -0.0595 | 0.3359 | 0.0702 | 0.2288 | -31.6062 | -26.1789 | -0.3111 | 9 | 0.2009 | -0.2222 | -0.0119 | 0.0821 | 0.074 | 0.2836 | 0.0225 | -0.449 | -0.2933 | 0.1015 | -0.0697 | -0.0468 | 0.1089 | -0.0861 | -0.0001 | 0.1371 | -0.0097 | 0.0009 | 0.1465 | 0.072 | 0.1811 | -15.1601 | -27.4241 | 3.3325 | 10 | 0.6172 | 0.4714 | 0.3391 | 0.5181 | -0.0179 | 1.3459 | 0.0081 | -0.1804 | 0.0242 | 0.1359 | -0.1237 | -0.0307 | -0.1731 | -0.0927 | -0.6446 | 0.0747 | -0.0198 | -0.0047 | 0.1078 | 0.0094 | 0.0661 | 3.2607 | -14.3713 | -3.0676 | 11 | 0.1805 | 0.1217 | 0.2672 | 0.2471 | 0.1043 | 0.496 | 0.0371 | 0.2767 | 0.0689 | -0.2081 | -0.4707 | 0.2497 | -0.1258 | -0.0736 | -0.0384 | 0.1846 | 0.0997 | -0.0237 | 0.1812 | -0.0197 | 0.1321 | -2.4295 | -4.7963 | -17.5866 | 12 | 1.0448 | 0.0938 | 0.2179 | 0.1879 | 0.0087 | 0.138 | 0.219 | -0.2934 | 0.0784 | 0.1656 | -0.1766 | 0.1049 | -0.0834 | -0.0344 | 0.0345 | 0.133 | -0.024 | 0.0307 | 0.1163 | -0.0183 | 0.0963 | -1.326 | -9.2944 | -2.0845 | 13 | 0.0345 | -0.128 | 0.1606 | 0.1075 | -0.0886 | 0.2249 | 0.2285 | 0.1104 | 0.3128 | -0.1254 | -0.1061 | 0.1278 | -0.1043 | -0.1101 | -0 | 0.1268 | -0.0061 | 0.0239 | 0.1076 | -0.0186 | 0.1516 | 2.5275 | -1.0388 | -11.5799 | 14 | 0.2024 | -0.1168 | -0.2157 | 0.1616 | -0.0444 | 0.1964 | 0.0708 | -0.045 | 0.0434 | 0.0786 | -0.0685 | 0.0058 | -0.0183 | 0.0018 | -0.0039 | 0.0831 | -0.0082 | -0.0008 | 0.0669 | 0.0006 | 0.0697 | 7.0807 | -10.9119 | -9.8294 | 15 | 0.026 | -0.08 | -0.1111 | 0.3321 | 0.1671 | 0.4845 | 0.0449 | 0.2164 | 0.0473 | -0.1743 | -0.0126 | 0.3734 | -0.0542 | -0.4259 | -0.0192 | 0.1344 | 0.0225 | -0.0167 | 0.1277 | 0.0021 | 0.1179 | -2.755 | -14.2325 | -22.3993 | 16 | 0.1025 | 0.1108 | 0.0463 | -0.0202 | -0.0362 | 0.0666 | 0.0043 | -0.0137 | 0.0445 | -0.0556 | -0.0569 | -0.0705 | 0.0053 | 0.0032 | -0 | 0.1138 | 0.0019 | 0.0095 | 0.0924 | -0.0043 | 0.094 | 10.0626 | -11.4536 | -18.0125 | 17 | 0.2961 | 0.0027 | -0.0081 | 0.052 | 0.0441 | 0.033 | -0.143 | -0.4286 | -0.0784 | 0.0272 | 0.0419 | -0.1493 | 0.0895 | 0.1487 | -0.0014 | 0.0847 | 0.0038 | 0.0004 | 0.1111 | -0.0055 | 0.1243 | 11.4346 | -18.4969 | -13.0752 | 18 | 0.3001 | -0.1211 | -0.2234 | 0.1263 | 0.186 | 0.1885 | 0.082 | 0.2667 | 0.0313 | -0.1071 | 0.0451 | 0.0289 | -0.053 | -0.1847 | 0.008 | 0.0795 | -0.0032 | -0.0077 | 0.1275 | 0.0122 | 0.1148 | -9.317 | -18.721 | -10.3987 | 19 | 0.0645 | -0.0198 | -0.0626 | 0.0237 | 0.0394 | 0.0508 | 0.0082 | 0.2381 | -0.3661 | -0.1537 | -0.0446 | 0.1227 | 0.069 | 0.0777 | -0 | 0.1245 | 0.0045 | -0.0088 | 0.1283 | 0.0082 | 0.1427 | -5.6884 | -24.2691 | -4.9357 | 20 | 0.0459 | 0.0115 | -0.0097 | 0.0082 | 0.3528 | 0.2583 | 0.0385 | 0.035 | -0.0893 | 0.0299 | 0.1648 | -0.4317 | -0.0584 | 1.1032 | 0.1473 | 0.1162 | 0.0178 | -0.0037 | 0.3265 | -0.0113 | 0.1265 | 6.3289 | -24.1578 | -3.4081 | 21 | 0.0289 | 0.1419 | 0.0222 | 0.1528 | 0.2308 | 0.2883 | 0.2877 | -0.4534 | 0.5959 | 0.0657 | -0.127 | 0.3422 | 0.0922 | 0.0261 | 0.0033 | 0.1233 | 0.026 | 0.0599 | 0.2788 | -0.0882 | 0.3732 | -14.9826 | -9.9032 | -41.7093 | 22 | 0.3285 | 0.1151 | -0.0075 | 0.0981 | -0.0382 | 0.0559 | 0.2552 | -0.5824 | 0.5063 | 0.1868 | -0.2752 | 0.3461 | -0.1025 | -0.0116 | 0.0473 | 0.1681 | 0.0148 | 0.0654 | 0.272 | -0.1421 | 0.3983 | -13.0227 | -7.4432 | -39.3176 | 23 | 0.0089 | 0.0064 | -0.0036 | 0.0053 | 0.0078 | 0.0196 | 0.0936 | -0.4596 | 0.2109 | 0.2806 | -0.1582 | -0.0298 | -0.2369 | -0.068 | 0 | 0.36 | -0.0483 | 0.0749 | 0.6787 | -0.3828 | 0.4709 | -9.4165 | -7.2561 | -31.2733 | 24 | 0.2292 | -0.0728 | 0.7563 | 0.0776 | 0.2479 | 1.5279 | 0.1055 | -0.8002 | 0.0162 | 0.1795 | -0.0678 | -0.2735 | 0.5823 | -0.172 | 0.0488 | 0.1474 | -0.0388 | 0.1399 | 0.6305 | -0.2182 | 0.3879 | -18.2163 | -13.2322 | -32.5095 | 25 | -0.016 | -0.0205 | -0.0103 | 0.0016 | -0.0365 | 0.0689 | 0.1921 | -0.8991 | -0.0416 | 0.5053 | -0.3113 | 0.3412 | 0.0279 | -0.2743 | -0 | 0.2402 | -0.0343 | 0.0982 | 0.519 | 0.0272 | 0.4604 | -24.9577 | -17.2589 | -37.4656 | 26 | 0.1175 | 0.0246 | 0.016 | 0.0179 | 0.0218 | 0.1271 | 0.009 | -0.0366 | -0.0446 | -0.1025 | 0.082 | 0.1593 | 0.105 | -0.3278 | 0.0023 | 0.0931 | 0.017 | 0.0071 | 0.2557 | 0.0061 | 0.2904 | -18.3581 | -14.9819 | -44.4709 | 27 | 0.0645 | -0.0298 | -0.0684 | 0.1047 | 0.0916 | 0.0898 | 0.0276 | 0.5467 | -0.3025 | -0.1016 | -0.4105 | 0.4191 | 0.244 | -0.0286 | -0.0007 | 0.1641 | -0.0122 | -0.017 | 0.4084 | -0.0342 | 0.4415 | -24.9143 | -20.1635 | -46.1924 | 28 | 0.2736 | 0.3959 | 0.0604 | 0.3361 | 0.1267 | 0.071 | 0.1389 | 0.1631 | -0.0272 | 0.014 | -0.1263 | 0.0841 | 0.1874 | -0.1149 | 0.0007 | 0.1116 | 0.0003 | -0.0065 | 0.1804 | 0.0121 | 0.1379 | -6.1004 | -16.8351 | -48.1235 | 29 | 0.0575 | -0.0077 | 0.0252 | 0.0903 | 0.0514 | 0.1913 | 0.0003 | 0.5161 | 0.6599 | -0.2046 | 0.0364 | 0.27 | -0.3122 | -0.2057 | 0.01 | 0.1871 | 0.0528 | -0.0407 | 0.2134 | 0.0909 | 0.3118 | -4.1871 | -4.3376 | -52.9003 | 30 | 0.0692 | -0.0063 | 0.0069 | 0.0046 | -0.0384 | 0.1309 | 0.1252 | 0.0683 | 0.0591 | -0.0261 | -0.057 | -0.1107 | -0.1853 | 0.1573 | 0.0004 | 0.1512 | -0.0084 | -0.0113 | 0.1116 | 0.0053 | 0.1053 | 7.6346 | -12.1779 | -45.1663 | 31 | 0.0918 | -0.191 | 0.102 | 0.5185 | 0.0516 | 0.2703 | -0.147 | 0.1698 | 0.0939 | -0.0511 | 0.0565 | -0.0103 | -0.0031 | -0.0392 | -0.0012 | 0.0802 | -0.0015 | 0.0032 | 0.1041 | 0.0095 | 0.0892 | 9.2151 | -28.8462 | -31.8128 | 32 | 0.1539 | 0.1145 | -0.1524 | -0.4457 | -0.3244 | -0.0072 | -0.1613 | -0.2281 | -0.0951 | 0.4016 | -0.1051 | 0.8197 | 0.0539 | -0.4566 | -0.0698 | 0.1844 | -0.0295 | 0.1471 | 0.2358 | -0.0516 | 0.3094 | -6.8537 | -35.7183 | -23.8814 | 33 | 0.7164 | -0.1478 | 0.1022 | 0.6146 | -0.165 | 0.4948 | -0.0122 | 0.0466 | 0.0041 | -0.0571 | -0.0211 | -0.0033 | 0.0703 | -0.0411 | -0.3039 | 0.1035 | -0.0084 | 0.0054 | 0.0786 | -0.0176 | 0.073 | 4.3614 | -32.7135 | -35.8845 | 34 | 0.1349 | -0.0063 | 0.0599 | 0.04 | -0.0602 | 0.2278 | -0.0485 | -0.0042 | -0.0816 | 0.0593 | 0.0156 | -0.0065 | 0.0904 | -0.0145 | -0.0278 | 0.123 | 0.0013 | 0.0082 | 0.0693 | -0.0074 | 0.0969 | 5.7241 | -36.7752 | -24.723 | 35 | 0.0069 | 0.0465 | -0.1359 | -0.0126 | -0.0379 | 0.2968 | 0.0362 | 0.1106 | 0.0998 | 0.1492 | -0.0454 | 0.2512 | -0.1711 | -0.5198 | 0.0024 | 0.1154 | -0.0181 | 0.0122 | 0.1426 | -0.0115 | 0.1107 | -5.239 | -24.3287 | -21.1441 | 36 | 0.2797 | -0.6427 | -0.041 | 1.0109 | 0.2732 | 0.3629 | -0.1106 | 0.0112 | -0.0385 | 0.2954 | -0.0237 | 0.1002 | 0.2107 | -0.0312 | -0.0839 | 0.1709 | 0.0124 | 0.0135 | 0.081 | -0.006 | 0.0941 | 5.7939 | -32.3278 | -16.5426 | 37 | 0.2875 | -0.0354 | -0.0444 | 0.1146 | 0.1443 | 0.0902 | -0.2208 | -0.0089 | 0.0727 | 0.1689 | 0.0571 | -0.1703 | -0.0381 | -0.0056 | -0.0108 | 0.1228 | 0.0138 | -0.0174 | 0.0744 | 0.0034 | 0.1071 | 9.6807 | -25.0331 | -20.2298 | 38 | 0.0136 | -0.0371 | 0.0225 | 0.0581 | 0.0451 | 0.0793 | -0.1444 | 0.0102 | 0.0508 | 0.0316 | -0.0423 | 0.2999 | 0.2283 | -0.515 | -0.0022 | 0.104 | 0.008 | -0.0134 | 0.1726 | 0.0033 | 0.13 | -2.4468 | -19.4158 | -30.7313 | 39 | 0.3381 | 0.0573 | 0.1996 | 0.1787 | -0.2177 | 0.3209 | -0.0579 | -0.1545 | 0.189 | -0.0044 | 0.01 | -0.0379 | -0.0558 | -0.115 | -0.0006 | 0.125 | -0.0096 | -0.0035 | 0.102 | -0.0159 | 0.0917 | 4.6007 | -17.4455 | -35.7524 | 40 | 0.1355 | 0.4646 | -0.2563 | 0.2947 | -0.1777 | 0.4494 | -0.0139 | -0.1288 | -0.2738 | 0.4625 | 0.1108 | -0.6662 | 0.1739 | 0.8352 | -0.0561 | 0.1963 | -0.0226 | -0.0913 | 0.2171 | -0.0106 | 0.1813 | 16.0083 | -21.1199 | -27.8161 |
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Refinement TLS group | 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 26:32)A26 - 32 | 2 | X-RAY DIFFRACTION | 2 | (chain A and resid 33:56)A33 - 56 | 3 | X-RAY DIFFRACTION | 3 | (chain A and resid 57:63)A57 - 63 | 4 | X-RAY DIFFRACTION | 4 | (chain A and resid 64:75)A64 - 75 | 5 | X-RAY DIFFRACTION | 5 | (chain A and resid 76:86)A76 - 86 | 6 | X-RAY DIFFRACTION | 6 | (chain A and resid 87:111)A87 - 111 | 7 | X-RAY DIFFRACTION | 7 | (chain A and resid 112:131)A112 - 131 | 8 | X-RAY DIFFRACTION | 8 | (chain A and resid 132:136)A132 - 136 | 9 | X-RAY DIFFRACTION | 9 | (chain A and resid 137:153)A137 - 153 | 10 | X-RAY DIFFRACTION | 10 | (chain A and resid 154:165)A154 - 165 | 11 | X-RAY DIFFRACTION | 11 | (chain A and resid 166:176)A166 - 176 | 12 | X-RAY DIFFRACTION | 12 | (chain A and resid 177:198)A177 - 198 | 13 | X-RAY DIFFRACTION | 13 | (chain A and resid 199:206)A199 - 206 | 14 | X-RAY DIFFRACTION | 14 | (chain A and resid 207:219)A207 - 219 | 15 | X-RAY DIFFRACTION | 15 | (chain A and | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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