Software | Name | Version | Classification |
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XDS | | data reductionXSCALE | | data scalingPHENIX | 1.14_3247refinementPDB_EXTRACT | 3.24 | data extractionPHASER | | phasingARP/wARP | | model building Coot | | model building | | | | | | | |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→49.575 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.34
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1755 | 1905 | 1.45 % | 0 |
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Rwork | 0.1494 | - | - | - |
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obs | 0.1498 | 131039 | 96.72 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å |
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Displacement parameters | Biso max: 78.14 Å2 / Biso mean: 25.0433 Å2 / Biso min: 9.56 Å2 |
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Refinement step | Cycle: final / Resolution: 1.6→49.575 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 6701 | 0 | 204 | 1248 | 8153 |
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Biso mean | - | - | 17.73 | 36.95 | - |
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Num. residues | - | - | - | - | 862 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.007 | 7415 | X-RAY DIFFRACTION | f_angle_d0.978 | 10173 | X-RAY DIFFRACTION | f_dihedral_angle_d13.408 | 4641 | X-RAY DIFFRACTION | f_chiral_restr0.054 | 1117 | X-RAY DIFFRACTION | f_plane_restr0.006 | 1419 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Num. reflection all | % reflection obs (%) |
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1.6-1.64 | 0.2512 | 122 | 0.1983 | 8455 | 8577 | 89 | 1.64-1.6844 | 0.2162 | 114 | 0.177 | 9025 | 9139 | 95 | 1.6844-1.7339 | 0.2108 | 144 | 0.1656 | 9075 | 9219 | 95 | 1.7339-1.7899 | 0.1865 | 159 | 0.1587 | 9110 | 9269 | 96 | 1.7899-1.8539 | 0.1995 | 117 | 0.1619 | 9257 | 9374 | 97 | 1.8539-1.9281 | 0.1823 | 146 | 0.1596 | 9399 | 9545 | 99 | 1.9281-2.0159 | 0.174 | 153 | 0.1594 | 9388 | 9541 | 99 | 2.0159-2.1221 | 0.1769 | 165 | 0.1535 | 9310 | 9475 | 98 | 2.1221-2.2551 | 0.1792 | 123 | 0.1505 | 9396 | 9519 | 98 | 2.2551-2.4292 | 0.1907 | 130 | 0.153 | 9312 | 9442 | 98 | 2.4292-2.6736 | 0.2264 | 142 | 0.1554 | 9325 | 9467 | 97 | 2.6736-3.0605 | 0.164 | 115 | 0.1521 | 9273 | 9388 | 97 | 3.0605-3.8557 | 0.1599 | 118 | 0.1363 | 9309 | 9427 | 97 | 3.8557-49.5988 | 0.1468 | 157 | 0.1373 | 9500 | 9657 | 98 |
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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 | 3.134 | 0.4949 | -0.9387 | 1.4334 | -0.391 | 2.2521 | -0.0491 | 0.1265 | -0.1419 | -0.0131 | -0.0487 | 0.07 | 0.2771 | -0.0474 | 0.0352 | 0.1882 | 0.0078 | -0.0067 | 0.1252 | -0.0097 | 0.107 | 45.8664 | 14.6099 | -5.0316 | 2 | 0.9736 | 0.0666 | -0.4632 | 1.9338 | -1.2604 | 2.0398 | -0.0028 | 0.0584 | -0.2014 | -0.0811 | -0.064 | 0.1417 | 0.3522 | 0.0889 | 0.0952 | 0.2683 | 0.0334 | 0.0061 | 0.1356 | -0.0332 | 0.175 | 49.3846 | 10.1065 | -13.6008 | 3 | 1.9897 | -1.7801 | -0.3863 | 2.2994 | 0.1738 | 1.5557 | -0.069 | 0.1591 | -0.4224 | -0.4276 | -0.1233 | -0.1916 | 0.5469 | 0.298 | 0.1236 | 0.3412 | 0.1023 | 0.0426 | 0.2057 | -0.0023 | 0.2106 | 57.5917 | 14.5221 | -24.9609 | 4 | 1.7106 | -0.4418 | -0.5281 | 4.1711 | -0.5961 | 2.9006 | 0.0218 | 0.1316 | 0.0187 | -0.777 | -0.0642 | 0.1017 | 0.0734 | 0.1874 | 0.0225 | 0.2405 | 0.0177 | -0.0299 | 0.167 | -0.0001 | 0.1237 | 52.9835 | 27.7511 | -26.8781 | 5 | 1.0718 | 0.5421 | -0.2631 | 2.3719 | -0.5206 | 2.0505 | 0.0233 | -0.0223 | 0.0259 | -0.243 | -0.0704 | 0.1262 | 0.0758 | 0.1113 | -0.0105 | 0.1635 | 0.0191 | -0.0182 | 0.1372 | -0.0074 | 0.17 | 50.0697 | 27.1918 | -19.3833 | 6 | 1.4673 | 1.0416 | -0.51 | 2.5034 | -0.6119 | 2.0187 | -0.0045 | 0.1289 | 0.0736 | 0.0042 | 0.0557 | 0.2506 | 0.1317 | -0.0954 | 0.0019 | 0.159 | -0.0019 | -0.0131 | 0.1601 | 0.0089 | 0.1645 | 46.2474 | 23.4578 | -10.1106 | 7 | 5.177 | -1.8044 | 0.5472 | 3.8443 | -1.1166 | 2.947 | -0.0537 | 0.0448 | 0.3627 | 0.1149 | 0.0593 | 0.2911 | -0.0577 | -0.0092 | 0.0224 | 0.1445 | 0.004 | -0.0022 | 0.1216 | 0.0182 | 0.1967 | 49.136 | 21.8789 | -4.196 | 8 | 1.696 | 0.3829 | -0.6659 | 1.6752 | -0.6379 | 2.048 | -0.0112 | -0.0684 | -0.0431 | -0.0475 | -0.1432 | -0.2839 | 0.1018 | 0.5247 | 0.1484 | 0.1546 | 0.0492 | -0.0232 | 0.2865 | 0.0342 | 0.1766 | 65.0696 | 19.116 | -6.8697 | 9 | 2.2963 | 0.1668 | -0.177 | 1.8839 | -0.4699 | 2.604 | -0.1529 | -0.186 | -0.2964 | 0.0438 | -0.0685 | -0.1086 | 0.3961 | 0.0924 | 0.0909 | 0.2198 | 0.0261 | 0.0342 | 0.1426 | 0.0165 | 0.1875 | 48.3581 | 8.4052 | 0.6526 | 10 | 4.8267 | 2.7078 | -1.2457 | 2.2436 | -1.0827 | 0.9262 | 0.1855 | -0.5429 | 0.1137 | 0.1145 | -0.3203 | -0.127 | -0.0587 | 0.5667 | 0.1857 | 0.1912 | 0.0011 | -0.0163 | 0.4741 | 0.0222 | 0.2051 | 67.0029 | 19.1797 | 1.7906 | 11 | 2.4424 | -0.0186 | 0.7011 | 0.8744 | 0.1086 | 1.717 | -0.0542 | 0.1533 | 0.1631 | -0.0144 | 0.0167 | -0.0669 | -0.2527 | 0.1161 | 0.0197 | 0.1706 | -0.0421 | 0.0056 | 0.1492 | 0.0074 | 0.1278 | 37.2325 | 60.928 | 37.4369 | 12 | 0.9077 | 0.4222 | 0.8761 | 2.3788 | 1.8191 | 2.9164 | -0.0295 | 0.1541 | 0.138 | -0.1158 | 0.0235 | -0.0851 | -0.4119 | 0.2371 | -0.0496 | 0.2236 | -0.0658 | 0.0038 | 0.1727 | 0.0143 | 0.1601 | 39.656 | 59.8677 | 29.262 | 13 | 2.2314 | -1.3853 | 0.1332 | 2.8727 | 0.1434 | 2.6166 | 0.0354 | 0.142 | 0.2239 | -0.2441 | -0.0356 | 0.1085 | -0.4271 | -0.1747 | 0.057 | 0.226 | 0.0174 | -0.013 | 0.1574 | 0.0089 | 0.2127 | 28.7906 | 57.8952 | 19.9579 | 14 | 1.3568 | -0.9903 | 0.3043 | 3.4532 | 0.3276 | 2.274 | 0.0484 | 0.1213 | -0.0659 | -0.5185 | -0.0751 | 0.0281 | 0.0055 | -0.0466 | -0.0174 | 0.1789 | -0.0132 | 0.013 | 0.1749 | -0.01 | 0.1472 | 33.6339 | 45.2051 | 18.1657 | 15 | 0.5207 | -0.268 | -0.0008 | 1.744 | 0.5122 | 2.0794 | -0.014 | -0.0025 | 0.0526 | -0.072 | -0.0252 | -0.014 | -0.0662 | 0.0841 | -0.0379 | 0.1184 | -0.0228 | 0.0025 | 0.1278 | 0.0006 | 0.1633 | 36.4928 | 45.9225 | 25.6996 | 16 | 0.9229 | 0.3338 | 0.4365 | 2.3207 | 0.523 | 1.946 | -0.0198 | 0.1725 | -0.0164 | 0.0047 | 0.1445 | -0.1238 | -0.0451 | 0.1651 | -0.0391 | 0.1365 | -0.0314 | 0.0034 | 0.1744 | -0.0172 | 0.1396 | 39.3343 | 48.9095 | 35.2642 | 17 | 6.1633 | -2.4016 | -1.0215 | 3.1692 | 1.0356 | 2.376 | -0.2075 | 0.2049 | -0.3201 | 0.1518 | 0.127 | -0.2186 | 0.0987 | 0.1329 | -0.0319 | 0.1425 | -0.0431 | 0.0096 | 0.1489 | -0.011 | 0.1826 | 37.2227 | 51.1416 | 40.8053 | 18 | 1.563 | -0.0738 | 0.266 | 1.7863 | 0.2556 | 3.8739 | -0.0507 | 0.1345 | 0.1104 | -0.2551 | 0.0758 | 0.3183 | -0.172 | -0.5766 | 0.164 | 0.1884 | 0.0103 | -0.0384 | 0.2611 | -0.0092 | 0.2085 | 16.2088 | 58.2253 | 33.2915 | 19 | 1.5387 | 0.6334 | 1.0365 | 1.4552 | 0.3987 | 2.6259 | 0.051 | -0.0609 | -0.0882 | 0.0578 | -0.1147 | 0.1187 | 0.1677 | -0.2943 | 0.0285 | 0.1631 | -0.0249 | 0.0372 | 0.2223 | -0.0081 | 0.1803 | 23.1704 | 50.8303 | 40.4255 | 20 | 2.1068 | -0.2989 | 0.254 | 1.3937 | 0.2772 | 1.9734 | -0.1185 | -0.0438 | 0.2206 | 0.155 | 0.013 | 0.0143 | -0.2253 | 0.0908 | 0.0262 | 0.2097 | -0.0315 | -0.0095 | 0.1423 | -0.0155 | 0.1651 | 37.7029 | 64.2382 | 46.0643 | 21 | 3.7172 | 1.9146 | 0.1195 | 2.2851 | 0.3935 | 1.5353 | 0.1361 | -0.2152 | -0.1759 | 0.1766 | -0.146 | 0.2068 | 0.1784 | -0.4109 | 0.0649 | 0.1983 | -0.0307 | 0.0252 | 0.2986 | -0.0059 | 0.2005 | 19.1617 | 53.0224 | 47.0043 | 22 | 2.4435 | -0.7532 | -0.4594 | 1.732 | 0.4995 | 1.9062 | -0.0699 | 0.0322 | -0.1225 | 0.001 | 0.0812 | -0.0811 | 0.2533 | 0.2396 | -0.0417 | 0.1655 | 0.0282 | -0.0076 | 0.151 | -0.0136 | 0.1307 | 33.3682 | 16.2477 | 14.678 | 23 | 0.3552 | 0.1888 | 0.0622 | 1.4665 | 0.3481 | 1.2783 | 0.0124 | -0.0538 | -0.0335 | 0.1271 | 0.0093 | -0.0656 | 0.098 | 0.1094 | -0.0369 | 0.1215 | 0.0199 | -0.0084 | 0.1294 | 0.0056 | 0.1483 | 31.0086 | 24.5799 | 27.4523 | 24 | 1.4473 | -0.0779 | -0.2506 | 2.0893 | 0.4084 | 1.6853 | -0.0226 | 0.0448 | 0.0909 | -0.0554 | 0.0062 | 0.1065 | -0.095 | -0.1029 | 0.0321 | 0.1301 | 0.0158 | -0.0398 | 0.1181 | 0.0152 | 0.1514 | 21.0368 | 27.3528 | 15.6567 | 25 | 1.9325 | -0.4103 | -0.1202 | 1.686 | 0.2511 | 2.082 | 0.0565 | 0.2437 | -0.1271 | -0.2377 | -0.0994 | 0.2194 | -0.0489 | -0.1296 | 0.0074 | 0.2026 | 0.0279 | -0.0307 | 0.1641 | -0.0132 | 0.1603 | 23.2041 | 18.9523 | 8.2687 | 26 | 2.8288 | -1.2772 | 0.2367 | 2.3249 | -0.4654 | 2.1789 | 0.0998 | 0.0978 | 0.1146 | -0.0001 | -0.0714 | 0.0054 | -0.2609 | 0.1175 | -0.0418 | 0.173 | -0.035 | 0.0252 | 0.1414 | 0.0052 | 0.1329 | 54.6554 | 55.548 | -29.7285 | 27 | 0.5758 | 0.1437 | -0.329 | 2.0126 | -0.6987 | 1.5323 | 0.0654 | -0.1209 | 0.098 | 0.2359 | -0.0833 | -0.1004 | -0.1967 | 0.3777 | 0.0027 | 0.1432 | -0.0575 | -0.0134 | 0.1784 | -0.0221 | 0.141 | 58.1592 | 48.9553 | -15.1753 | 28 | 1.3436 | -0.8385 | -0.1096 | 2.9702 | -0.8384 | 1.9102 | 0.0207 | -0.0377 | 0.003 | 0.0802 | 0.0692 | 0.1492 | -0.0539 | 0.1196 | -0.0502 | 0.1348 | -0.0206 | 0.0016 | 0.1371 | 0.0028 | 0.1392 | 51.9465 | 47.2668 | -25.0262 | 29 | 1.1212 | -0.1811 | 0.3386 | 2.4553 | -0.3774 | 2.1347 | -0.0089 | -0.0288 | -0.0259 | 0.0626 | -0.0007 | -0.1681 | 0.0181 | 0.3556 | 0.0747 | 0.1694 | 0.0031 | 0.0325 | 0.1996 | 0.0155 | 0.1819 | 65.6488 | 48.1029 | -27.4581 | 30 | 2.319 | -0.8455 | 1.7487 | 2.1891 | -1.4992 | 4.8252 | 0.1623 | -0.0554 | -0.3292 | -0.134 | -0.0415 | -0.3261 | 0.618 | 0.3092 | 0.0208 | 0.2616 | 0.0439 | 0.0465 | 0.2808 | -0.0224 | 0.2789 | 69.311 | 38.4301 | -27.9847 | 31 | 1.8978 | -0.422 | -0.1018 | 2.0672 | -0.2911 | 2.1385 | 0.0388 | 0.2258 | 0.044 | -0.1605 | -0.1658 | -0.3118 | 0.0744 | 0.3904 | 0.0401 | 0.188 | -0.017 | 0.026 | 0.2355 | 0.02 | 0.1668 | 64.2885 | 53.1427 | -36.4359 |
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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 2 through 23 )A2 - 23 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 24 through 46 )A24 - 46 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 47 through 59 )A47 - 59 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 60 through 73 )A60 - 73 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 74 through 98 )A74 - 98 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 99 through 121 )A99 - 121 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 122 through 137 )A122 - 137 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 138 through 183 )A138 - 183 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 184 through 203 )A184 - 203 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 204 through 217 )A204 - 217 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 3 through 34 )B3 - 34 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 35 through 46 )B35 - 46 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 47 through 59 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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