Software | Name | Version | Classification |
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XSCALE | | data scalingMOLREP | | phasingPHENIX | (dev_2443: ???)refinementPDB_EXTRACT | 3.2 | data extractionXDS | | data scalingCoot | | model building | | | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GHW Resolution: 1.6→49.072 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.78
| Rfactor | Num. reflection | % reflection |
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Rfree | 0.1919 | 1931 | 1.76 % |
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Rwork | 0.1647 | - | - |
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obs | 0.1652 | 109637 | 99.29 % |
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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: 86.15 Å2 / Biso mean: 30.2831 Å2 / Biso min: 13.22 Å2 |
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Refinement step | Cycle: final / Resolution: 1.6→49.072 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 5137 | 0 | 88 | 684 | 5909 |
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Biso mean | - | - | 52.14 | 38.74 | - |
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Num. residues | - | - | - | - | 659 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.006 | 5528 | X-RAY DIFFRACTION | f_angle_d0.873 | 7510 | X-RAY DIFFRACTION | f_chiral_restr0.061 | 816 | X-RAY DIFFRACTION | f_plane_restr0.007 | 994 | X-RAY DIFFRACTION | f_dihedral_angle_d13.451 | 3327 | | | | | |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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 | 0.2557 | 134 | 0.2284 | 7628 | 7762 | 100 | 1.64-1.6844 | 0.2206 | 142 | 0.2065 | 7607 | 7749 | 100 | 1.6844-1.7339 | 0.2156 | 164 | 0.1911 | 7666 | 7830 | 100 | 1.7339-1.7899 | 0.2046 | 124 | 0.1796 | 7658 | 7782 | 100 | 1.7899-1.8539 | 0.2064 | 127 | 0.1751 | 7695 | 7822 | 100 | 1.8539-1.9281 | 0.2241 | 145 | 0.1765 | 7706 | 7851 | 100 | 1.9281-2.0159 | 0.2424 | 147 | 0.1714 | 7629 | 7776 | 100 | 2.0159-2.1221 | 0.1819 | 149 | 0.1678 | 7711 | 7860 | 100 | 2.1221-2.2551 | 0.1935 | 141 | 0.1679 | 7700 | 7841 | 100 | 2.2551-2.4292 | 0.194 | 114 | 0.168 | 7727 | 7841 | 99 | 2.4292-2.6737 | 0.212 | 125 | 0.1743 | 7690 | 7815 | 99 | 2.6737-3.0605 | 0.2213 | 135 | 0.1749 | 7723 | 7858 | 99 | 3.0605-3.8557 | 0.1684 | 143 | 0.1544 | 7747 | 7890 | 98 | 3.8557-49.0949 | 0.165 | 141 | 0.1433 | 7819 | 7960 | 96 |
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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 | 6.2293 | -1.9185 | -5.2879 | 3.0825 | 4.1929 | 9.1066 | -0.1529 | -0.1867 | 0.1617 | 0.5107 | -0.0154 | 0.5303 | -0.6364 | -0.5863 | 0.1392 | 0.372 | 0.0633 | 0.0629 | 0.2114 | -0.0123 | 0.2488 | -24.0323 | 10.6157 | 3.3673 | 2 | 7.6279 | 2.8622 | -5.2235 | 4.1348 | -3.1268 | 3.9813 | -0.2146 | -0.4809 | -0.3359 | 0.1023 | -0.1887 | -0.0775 | 0.3052 | 0.2052 | 0.5319 | 0.2233 | -0.0052 | 0.0162 | 0.1596 | -0.0006 | 0.1181 | -19.1866 | -4.3261 | 11.3031 | 3 | 4.1267 | -1.9266 | 2.5584 | 5.6486 | -4.5501 | 3.9819 | -0.1008 | -0.152 | 0.1987 | 0.4113 | 0.1137 | 0.2241 | -0.5137 | -0.716 | -0.024 | 0.2195 | 0.0232 | 0.0663 | 0.2774 | -0.0297 | 0.2068 | -31.9231 | 2.6317 | 11.1215 | 4 | 1.2446 | 0.2389 | -0.4586 | 2.4366 | -0.26 | 2.1361 | -0.0455 | 0.217 | -0.024 | -0.1024 | -0.0363 | 0.4051 | 0.2456 | -0.5811 | 0.0679 | 0.1841 | -0.0419 | 0.0167 | 0.2714 | -0.0286 | 0.1814 | -31.0492 | -3.2544 | -0.2949 | 5 | 2.8994 | -0.6019 | 0.2393 | 4.2901 | -3.5158 | 4.0964 | -0.0781 | 0.346 | -0.402 | -0.3036 | -0.2386 | 0.0055 | 0.9367 | -0.1598 | 0.1794 | 0.3151 | -0.0615 | 0.0578 | 0.1939 | -0.0318 | 0.1987 | -25.9175 | -11.135 | -14.7655 | 6 | 1.7855 | 1.1094 | -0.1374 | 3.6549 | -0.2566 | 3.589 | 0.0165 | 0.0392 | 0.0298 | 0.0802 | -0.0069 | 0.1161 | 0.1541 | -0.3387 | 0.0084 | 0.0991 | -0.008 | 0.017 | 0.1402 | -0.0009 | 0.1134 | -26.3107 | 1.2136 | -10.9545 | 7 | 0.6524 | -0.0267 | 0.2987 | 0.9 | -1.8262 | 3.8462 | 0.052 | 0.0231 | -0.1092 | 0.3911 | -0.0382 | 0.2935 | 1.4828 | -0.5964 | 0.0779 | 0.4073 | -0.1471 | 0.0748 | 0.2197 | -0.0115 | 0.2582 | -28.77 | -14.0774 | 5.1517 | 8 | 2.3675 | 0.038 | 0.1266 | 1.2098 | -0.9498 | 3.2764 | -0.061 | -0.0269 | -0.1469 | 0.0902 | 0.013 | 0.1853 | 0.3381 | -0.3877 | 0.0064 | 0.2338 | -0.0393 | 0.0623 | 0.1342 | -0.015 | 0.1581 | -27.8602 | -9.396 | -2.837 | 9 | 2.6648 | 1.0479 | 2.3695 | 3.8185 | -0.4869 | 2.7505 | 0.1068 | 0.2228 | -0.0909 | 0.1401 | 0.0427 | -0.0679 | 0.395 | 0.7295 | -0.1301 | 0.1987 | 0.0281 | 0.0097 | 0.2062 | -0.007 | 0.1529 | -18.7455 | -0.5145 | -12.1284 | 10 | 4.3631 | -0.1114 | 0.2523 | 6.3277 | 1.2876 | 8.6937 | -0.0195 | 0.1442 | 0.2846 | -0.1086 | 0.0736 | 0.5913 | -0.2565 | -0.5649 | -0.0661 | 0.1265 | -0.0097 | 0.0003 | 0.21 | 0.0408 | 0.2051 | -28.8475 | 6.727 | -19.4195 | 11 | 6.7662 | 2.4858 | -3.0946 | 5.9968 | -2.2798 | 6.2043 | 0.1187 | -0.4446 | -0.3418 | 0.1167 | -0.2516 | 0.0782 | 0.2483 | -0.3022 | 0.1295 | 0.1526 | -0.0326 | -0.0021 | 0.2429 | 0.0112 | 0.1732 | -26.7124 | -5.426 | -34.7152 | 12 | 2.4873 | -1.2631 | 0.8928 | 5.4478 | -1.5061 | 1.5599 | -0.1787 | -0.4878 | -0.0664 | 0.5779 | 0.0882 | -0.1372 | 0.0081 | 0.0662 | 0.1222 | 0.2436 | 0.0162 | 0.0066 | 0.2874 | 0.0114 | 0.1138 | -12.7607 | -4.2014 | -22.7672 | 13 | 6.4325 | 0.8476 | 4.466 | 3.6372 | 2.4942 | 7.1289 | 0.2569 | -0.4096 | -0.7471 | -0.1459 | 0.2531 | 0.4719 | 1.2733 | -0.5835 | -0.4164 | 0.4748 | -0.061 | -0.0318 | 0.2069 | 0.1182 | 0.3427 | -20.3152 | -16.4088 | -26.4969 | 14 | 4.5339 | -0.8353 | -0.3482 | 5.0019 | 1.0782 | 3.6426 | 0.0377 | 0.2699 | -0.7622 | -0.2628 | -0.0291 | -0.0229 | 0.6622 | -0.0095 | 0.0432 | 0.2842 | 0.0181 | 0.0071 | 0.1573 | -0.0249 | 0.1983 | -15.5806 | -13.8396 | -34.0158 | 15 | 4.7389 | -0.0007 | -0.8275 | 2.577 | 0.4991 | 2.8124 | 0.029 | -0.1849 | -0.0167 | 0.2223 | 0.0324 | -0.1048 | 0.2093 | 0.231 | -0.0665 | 0.2258 | 0.0764 | -0.0063 | 0.2296 | -0.0047 | 0.1467 | -5.5137 | -8.6157 | -32.5079 | 16 | 9.7712 | 0.5904 | -0.0624 | 0.7326 | -0.313 | 1.0475 | -0.0532 | 0.2987 | -0.1183 | -0.0636 | 0.0216 | -0.0685 | 0.2516 | 0.1797 | 0.0543 | 0.2428 | 0.048 | 0.0001 | 0.1732 | -0.0078 | 0.1527 | -12.8818 | -9.0943 | -48.4932 | 17 | 4.6679 | 1.8069 | -5.7725 | 1.6581 | -2.7378 | 8.1407 | 0.0202 | -0.6814 | -0.2423 | 0.1959 | -0.0667 | 0.0615 | 0.1075 | 1.184 | 0.1528 | 0.2808 | 0.1611 | -0.0024 | 0.2753 | 0.0349 | 0.1947 | -3.8074 | -12.5353 | -30.5652 | 18 | 2.2016 | -0.3018 | 0.9092 | 0.8763 | 0.2168 | 3.6978 | -0.1228 | -0.1079 | -0.1688 | 0.0337 | 0.0621 | 0.0178 | 0.1032 | 0.2141 | 0.0598 | 0.1415 | 0.0274 | 0.0129 | 0.1742 | 0.0071 | 0.1244 | -10.4175 | -8.3363 | -41.5358 | 19 | 9.5763 | 3.1569 | -3.0231 | 6.216 | -1.5358 | 6.0962 | -0.078 | 0.3722 | -0.6092 | -0.1142 | 0.194 | 0.154 | 0.823 | -0.2261 | -0.1468 | 0.2856 | 0.0123 | -0.0641 | 0.1705 | -0.0274 | 0.1975 | -23.3839 | -11.1395 | -55.9815 | 20 | 3.7165 | -1.5911 | 1.0641 | 4.9875 | 0.0647 | 7.3616 | -0.1136 | 0.4558 | 0.5166 | -0.3353 | 0.2824 | 0.2482 | -0.4103 | -0.5451 | -0.1453 | 0.1254 | -0.0142 | -0.0254 | 0.2795 | 0.1053 | 0.2966 | -27.1011 | 15.1711 | -26.7223 | 21 | 1.9167 | 0.6719 | -1.4324 | 2.1768 | -1.8496 | 2.3522 | -0.1393 | 0.4063 | 0.4058 | -0.5523 | 0.3621 | 0.4103 | -0.4704 | -0.14 | -0.2021 | 0.3306 | -0.09 | -0.0541 | 0.28 | 0.1081 | 0.2756 | -19.2225 | 23.8683 | -32.8836 | 22 | 7.1855 | 3.2851 | -5.5623 | 6.1889 | -3.1885 | 6.4879 | 0.2017 | -0.4779 | 0.0745 | 0.4673 | -0.2027 | 0.1132 | -0.6149 | 0.6558 | -0.0429 | 0.3222 | -0.1331 | 0.0308 | 0.2326 | -0.0158 | 0.2277 | -10.5188 | 26.5223 | -17.2302 | 23 | 4.241 | 2.3331 | 2.3115 | 3.6171 | -1.5227 | 5.0305 | -0.2391 | 0.5875 | 0.0327 | -0.6239 | 0.2883 | 0.0664 | -0.1908 | 0.6095 | 0.009 | 0.2233 | -0.1585 | 0.039 | 0.3318 | -0.0047 | 0.1565 | -8.1183 | 20.6128 | -34.1517 | 24 | 9.3777 | -1.5026 | -6.0782 | 1.7963 | 0.85 | 3.9764 | -0.1256 | -0.3379 | -0.2404 | 0.0758 | 0.1766 | -0.5608 | 0.2849 | 1.1016 | 0.0042 | 0.1652 | 0.0395 | 0.0163 | 0.4946 | -0.0278 | 0.3472 | -1.9744 | 12.297 | -19.8249 | 25 | 1.8059 | 1.1968 | -0.7604 | 2.0267 | -0.8914 | 2.3701 | -0.0391 | 0.2102 | 0.0586 | -0.3375 | 0.2038 | -0.1242 | -0.2366 | 0.4209 | -0.1259 | 0.2059 | -0.0686 | 0.0283 | 0.2624 | -0.0174 | 0.1869 | -10.0697 | 18.6969 | -27.0243 | 26 | 3.0866 | 1.5066 | -1.459 | 2.6288 | 0.0546 | 2.0494 | -0.0654 | 0.0839 | -0.0359 | -0.1278 | 0.1533 | -0.1782 | -0.1791 | 0.5178 | -0.0024 | 0.1253 | -0.0497 | 0.0045 | 0.251 | -0.0028 | 0.1566 | -9.8958 | 14.6935 | -24.8771 | 27 | 7.3647 | 2.9868 | 2.8004 | 3.5435 | 5.5065 | 9.3895 | -0.1482 | -0.3263 | 0.6659 | 0.0241 | 0.2831 | 0.2063 | -0.8114 | 0.3155 | -0.1477 | 0.2989 | -0.0284 | 0.0368 | 0.1764 | -0.0134 | 0.2276 | -16.919 | 17.2553 | -6.8271 | 28 | 6.819 | 2.4829 | 0.067 | 4.5391 | 1.8677 | 4.9409 | 0.1027 | 0.2515 | -0.0775 | -0.2673 | 0.0203 | 0.4743 | 0.6288 | -0.348 | -0.1174 | 0.2607 | -0.025 | -0.0838 | 0.1441 | 0.0027 | 0.2294 | -31.3702 | -8.7585 | -63.3308 | 29 | 4.4563 | -0.6325 | 2.7413 | 1.7008 | -0.7348 | 2.5324 | 0.4612 | 0.9965 | -0.2916 | -0.4551 | -0.1716 | 0.2071 | 0.5539 | 0.1008 | -0.2354 | 0.3519 | 0.0353 | -0.0899 | 0.4266 | -0.0329 | 0.208 | -33.2202 | -0.3335 | -78.5423 | 30 | 4.4461 | -0.7985 | 3.0279 | 3.0109 | -1.8136 | 7.9221 | 0.1362 | -0.2409 | -0.6752 | -0.321 | 0.3874 | 0.9929 | 0.6574 | -1.1281 | -0.3651 | 0.3001 | -0.1088 | -0.1664 | 0.47 | 0.0891 | 0.5637 | -44.6529 | -3.1963 | -70.5676 | 31 | 5.664 | -0.1461 | 0.7054 | 5.4039 | -2.8763 | 8.2936 | 0.1764 | -0.0678 | -0.0917 | 0.0914 | 0.185 | 0.414 | 0.1614 | -0.337 | -0.2374 | 0.2274 | -0.0196 | -0.0713 | 0.1618 | 0.0116 | 0.2239 | -36.1178 | -2.1654 | -67.0481 | 32 | 2.2687 | -2.981 | -3.0788 | 4.0701 | 3.8461 | 4.5037 | -0.0297 | -0.1897 | -0.1715 | 0.1234 | -0.1242 | 0.7884 | 0.3296 | -1.1108 | 0.1751 | 0.179 | 0.0369 | -0.0264 | 0.4544 | 0.0045 | 0.341 | -41.9345 | 7.4167 | -65.6774 | 33 | 3.6787 | -0.4649 | -0.1731 | 3.1629 | 0.0552 | 4.5466 | -0.0086 | 0.2687 | 0.2512 | -0.1099 | 0.0678 | 0.0014 | -0.3589 | -0.0791 | -0.0303 | 0.1996 | 0.0463 | -0.0343 | 0.2266 | 0.0253 | 0.2251 | -33.4854 | 10.5718 | -71.5791 | 34 | 7.6598 | 4.644 | -4.0989 | 4.6061 | -0.5977 | 4.2642 | 0.3108 | -0.3172 | 0.4876 | 0.2677 | -0.2176 | 0.2225 | -0.9204 | 0.5643 | -0.0368 | 0.3716 | -0.0368 | -0.0628 | 0.2331 | -0.0268 | 0.2852 | -27.3921 | 15.4428 | -55.3984 | 35 | 1.8907 | -0.0737 | -0.0814 | 6.4154 | -3.1797 | 6.7617 | -0.0505 | -0.0903 | 0.0657 | 0.005 | -0.0188 | 0.1377 | -0.1221 | -0.2432 | 0.0457 | 0.119 | 0.0194 | -0.0295 | 0.1782 | -0.0227 | 0.1688 | -30.6452 | 3.2913 | -54.0867 | 36 | 3.9605 | 1.6335 | 1.817 | 5.811 | 3.9275 | 7.141 | -0.2048 | 0.4468 | 0.4223 | -0.4514 | 0.1553 | 0.4195 | -0.7472 | -0.2663 | 0.0403 | 0.3192 | 0.0788 | -0.0805 | 0.2401 | 0.0774 | 0.2928 | -37.2347 | 13.0971 | -73.0975 | 37 | 2.1482 | -0.7027 | 0.9092 | 2.9692 | -1.4195 | 4.8557 | -0.0144 | -0.0399 | 0.1692 | 0.0435 | 0.0703 | 0.1655 | -0.3475 | -0.3018 | -0.0664 | 0.1656 | 0.0102 | -0.0306 | 0.1405 | -0.0071 | 0.1783 | -30.885 | 8.7419 | -62.0551 | 38 | 2.4122 | 2.0002 | -3.2122 | 9.7867 | 0.1746 | 5.5535 | 0.3119 | -0.305 | 0.0881 | 0.6052 | -0.1226 | 0.5607 | -0.3312 | -0.6402 | -0.1988 | 0.2391 | 0.0459 | -0.0103 | 0.3375 | 0.0078 | 0.2118 | -30.4124 | 1.0081 | -43.9072 |
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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 0 through 13 )A0 - 13 | 2 | X-RAY DIFFRACTION | 2 | chain 'A' and (resid 14 through 25 )A14 - 25 | 3 | X-RAY DIFFRACTION | 3 | chain 'A' and (resid 26 through 41 )A26 - 41 | 4 | X-RAY DIFFRACTION | 4 | chain 'A' and (resid 42 through 87 )A42 - 87 | 5 | X-RAY DIFFRACTION | 5 | chain 'A' and (resid 88 through 97 )A88 - 97 | 6 | X-RAY DIFFRACTION | 6 | chain 'A' and (resid 98 through 112 )A98 - 112 | 7 | X-RAY DIFFRACTION | 7 | chain 'A' and (resid 113 through 125 )A113 - 125 | 8 | X-RAY DIFFRACTION | 8 | chain 'A' and (resid 126 through 147 )A126 - 147 | 9 | X-RAY DIFFRACTION | 9 | chain 'A' and (resid 148 through 157 )A148 - 157 | 10 | X-RAY DIFFRACTION | 10 | chain 'A' and (resid 158 through 169 )A158 - 169 | 11 | X-RAY DIFFRACTION | 11 | chain 'B' and (resid 1 through 14 )B1 - 14 | 12 | X-RAY DIFFRACTION | 12 | chain 'B' and (resid 15 through 25 )B15 - 25 | 13 | X-RAY DIFFRACTION | 13 | chain 'B' and (resid 26 through 42 )B | | | | | | | | | | | | | | | | | | | | | | | | | |
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