Software Name Version Classification PHENIX1.9_1692refinement XSCALEdata scaling PDB_EXTRACT3.22 data extraction XDSdata reduction PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENT / Resolution : 2.194→49.041 Å / SU ML : 0.21 / Cross valid method : FREE R-VALUE / σ(F) : 1.36 / Phase error : 21.1 Rfactor Num. reflection % reflection Rfree 0.1929 4212 5 % Rwork 0.1722 - - obs 0.1732 84222 99.72 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 ÅDisplacement parameters Biso max : 154.51 Å2 / Biso mean : 63.0572 Å2 / Biso min : 20 Å2 Refinement step Cycle : final / Resolution : 2.194→49.041 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6638 0 70 235 6943 Biso mean - - 75.26 54.41 - Num. residues - - - - 886
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.005 6955 X-RAY DIFFRACTION f_angle_d0.873 9487 X-RAY DIFFRACTION f_chiral_restr0.035 1052 X-RAY DIFFRACTION f_plane_restr0.004 1248 X-RAY DIFFRACTION f_dihedral_angle_d12.292 2433
Refine LS restraints NCS Ens-ID Dom-ID Auth asym-ID Number Refine-ID Rms Type 1 1 A2778 X-RAY DIFFRACTION 4.91 TORSIONAL1 2 B2778 X-RAY DIFFRACTION 4.91 TORSIONAL2 1 C1074 X-RAY DIFFRACTION 4.91 TORSIONAL2 2 D1074 X-RAY DIFFRACTION 4.91 TORSIONAL
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0 / Total num. of bins used : 30
Show large table (7 x 30) Hide large table Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Num. reflection all % reflection obs (%)2.1942-2.2192 0.2849 129 0.2599 2452 2581 94 2.2192-2.2453 0.2777 140 0.2326 2651 2791 100 2.2453-2.2727 0.2275 136 0.2295 2602 2738 100 2.2727-2.3014 0.2485 137 0.2363 2605 2742 100 2.3014-2.3317 0.2829 141 0.2292 2678 2819 100 2.3317-2.3637 0.2984 137 0.215 2591 2728 100 2.3637-2.3974 0.2546 139 0.2096 2641 2780 100 2.3974-2.4332 0.2235 140 0.2015 2640 2780 100 2.4332-2.4712 0.2347 139 0.1975 2633 2772 100 2.4712-2.5117 0.2582 139 0.2067 2641 2780 100 2.5117-2.5551 0.2634 140 0.2039 2653 2793 100 2.5551-2.6015 0.2357 138 0.1975 2637 2775 100 2.6015-2.6516 0.229 138 0.1962 2615 2753 100 2.6516-2.7057 0.2577 139 0.1951 2662 2801 100 2.7057-2.7645 0.2099 140 0.1796 2656 2796 100 2.7645-2.8288 0.2282 140 0.1903 2657 2797 100 2.8288-2.8995 0.1899 138 0.1891 2651 2789 100 2.8995-2.9779 0.2234 141 0.186 2664 2805 100 2.9779-3.0655 0.2027 140 0.1883 2667 2807 100 3.0655-3.1645 0.2405 141 0.1859 2674 2815 100 3.1645-3.2775 0.1873 140 0.1948 2661 2801 100 3.2775-3.4087 0.2322 141 0.1848 2683 2824 100 3.4087-3.5638 0.1783 142 0.1836 2683 2825 100 3.5638-3.7517 0.2206 141 0.1693 2671 2812 100 3.7517-3.9866 0.1858 143 0.1633 2724 2867 100 3.9866-4.2943 0.157 142 0.1389 2695 2837 100 4.2943-4.7261 0.1339 144 0.1196 2729 2873 100 4.7261-5.4092 0.1557 145 0.1386 2747 2892 100 5.4092-6.8122 0.1612 148 0.1586 2798 2946 100 6.8122-49.0537 0.1702 154 0.1748 2949 3103 99
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 25) Hide large table 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)1 3.0885 0.0215 -0.7331 3.3865 -1.2849 3.7018 -0.0041 0.3891 -0.2794 -0.1384 -0.0522 -0.0188 -0.0639 -0.1494 0.0805 0.2693 0.0231 -0.0551 0.5129 -0.0349 0.3119 0.6664 39.9474 -37.6771 2 6.6055 -4.5222 4.9007 4.2135 -5.2533 8.5477 -0.0189 -0.2832 0.0085 -0.0094 0.0672 0.0669 0.1094 -0.4231 -0.0103 0.2741 -0.0475 -0.0083 0.4424 -0.0538 0.312 2.3425 32.1183 -22.2796 3 2.8708 -0.6188 1.026 0.606 -1.2695 3.0831 0.0855 -0.0335 -0.1392 0.1166 -0.1562 -0.0027 0.1179 -0.152 0.1027 0.3371 -0.0962 -0.0446 0.5473 -0.0276 0.4577 2.6012 24.0618 -20.3488 4 4.2234 1.6615 1.2322 3.2811 0.7577 2.8776 0.0111 -0.1922 -0.3085 0.2223 -0.179 -0.3285 0.2162 0.4682 0.1268 0.2552 0.0462 -0.0667 0.477 0.0618 0.4443 13.969 23.2896 -19.7518 5 2.0827 0.2011 0.0314 1.3651 -0.4088 2.9816 0.0682 0.1905 -0.3537 0.0092 -0.098 -0.0159 0.3097 -0.1802 -0.0229 0.2472 -0.0116 -0.0392 0.4707 -0.0888 0.3971 4.2523 25.4247 -32.2303 6 3.9255 -0.7037 0.5627 2.1915 -0.0691 3.8352 0.0235 0.4477 0.1788 -0.1376 -0.1188 0.021 -0.4314 -0.3117 0.0986 0.3213 0.0676 -0.0233 0.6099 0.0097 0.3435 -2.4274 46.71 -40.8326 7 8.0539 0.1032 4.2658 4.1028 3.2159 8.4148 -0.4157 0.3293 0.6655 -0.4434 -0.1221 0.4423 -0.8263 -1.1278 0.5613 0.5866 0.1916 0.0031 0.7556 0.1211 0.3932 -8.9379 51.0952 -45.4968 8 3.1232 0.2105 -0.6343 1.4785 0.3817 2.5015 0.1005 -0.3918 0.2516 0.3702 -0.2159 -0.3264 -0.7325 0.5498 0.0705 0.5476 -0.1822 -0.0883 0.5227 0.0252 0.3719 14.437 50.0644 -16.7274 9 5.9972 -3.7622 -2.4159 2.6046 0.721 2.8451 0.0451 0.3595 -0.1775 0.2455 -0.3311 -0.2862 -0.5516 0.6066 0.0003 0.3493 -0.1297 -0.091 0.6699 0.126 0.4038 21.536 46.0029 -31.9383 10 1.0259 -0.1566 -0.8061 0.9796 1.3933 2.3349 -0.002 0.2645 0.09 -0.1752 -0.1233 -0.1687 -0.3146 0.9876 0.1433 0.4161 -0.1793 -0.0818 1.0019 0.1371 0.5516 29.6243 42.6854 -33.7181 11 7.1341 2.8146 2.5466 4.1406 0.7176 1.6561 -0.1612 0.5156 -0.4648 -0.2796 -0.0365 -0.4649 -0.2159 1.1055 0.068 0.258 0.0287 0.0081 0.8372 0.0587 0.4965 25.9209 31.8363 -35.1906 12 0.8978 1.0821 -0.3296 2.1462 0.0983 1.8017 -0.0797 0.015 -0.1299 0.1798 -0.1115 -0.5397 0.0735 0.9045 0.0875 0.2997 -0.0428 -0.103 0.9745 0.0969 0.5875 29.7136 34.0554 -28.5535 13 5.5686 0.3269 0.1152 2.5799 -1.107 0.4941 0.1214 0.2978 0.4517 0.3373 -0.2077 -0.797 -0.9696 0.8656 -0.069 0.6119 -0.478 -0.1715 1.0405 0.1123 0.6658 31.8912 52.3141 -24.2827 14 2.7959 -0.232 -0.5015 0.101 0.529 2.9089 -0.0473 -0.4311 0.1465 0.635 -0.0891 -0.1146 -0.6448 0.7608 0.0032 0.6422 -0.2559 -0.1739 0.7163 0.035 0.4279 20.1962 47.0815 -10.4341 15 1.9684 -0.3469 -0.7626 5.311 -0.1879 4.8867 0.1332 -0.0147 0.2416 0.231 -0.1147 0.1844 -1.1809 0.1273 0.0307 0.6227 -0.1294 -0.0614 0.4471 -0.004 0.3812 7.4252 56.0566 -15.7995 16 5.0118 1.0461 -0.1401 3.1617 0.9652 4.7629 -0.014 -0.0105 0.4404 0.8369 -0.0559 -0.0791 -0.7798 0.5979 0.153 0.6925 -0.1544 -0.1617 0.5152 -0.0108 0.377 13.0334 52.9163 -7.5281 17 3.5557 2.5697 4.9371 7.2692 2.7835 7.0042 -0.1125 -0.37 0.5342 0.0222 -0.1227 0.139 -1.7373 0.2847 0.3347 0.9985 -0.1308 0.0538 0.6101 -0.0305 0.4596 7.4478 62.8512 -8.7962 18 2.7189 -0.4078 0.7909 4.4635 -0.347 2.0907 0.2434 0.4667 -0.577 -0.4053 -0.1762 -0.7401 0.1059 0.1686 0.0247 0.4532 0.0432 0.0642 1.0364 0.1186 0.5476 25.7346 43.7682 -56.1103 19 7.1316 -1.7208 -1.7898 3.5863 0.0771 4.0396 0.2259 1.1669 0.1906 -0.5808 -0.2229 -0.5817 -0.2898 0.6704 -0.0045 0.5191 -0.0139 0.114 1.066 0.1489 0.5759 27.2623 47.0695 -61.6216 20 4.178 2.7517 -5.4979 9.7119 -6.1852 8.4885 0.4938 1.5381 1.8091 -0.9574 0.2905 1.5435 -0.862 -1.3341 -0.7262 0.9446 0.1738 0.0178 1.1131 0.1553 0.7205 13.7804 54.0648 -59.4972 21 7.4114 1.3629 -1.6803 3.9788 0.9733 2.4161 0.14 0.0051 -0.1697 0.1847 -0.2431 -0.5343 -0.3392 0.4724 0.1115 0.4012 -0.0161 -0.0367 0.9052 0.1371 0.5277 25.7925 48.5631 -50.4399 22 3.6099 5.1905 -0.7247 8.4144 0.4923 7.5398 0.4629 -0.5482 -1.2959 -0.057 -0.3251 -0.7903 0.6181 -0.1537 0.1266 0.7088 -0.098 -0.2181 0.6361 0.1905 0.8234 4.2815 21.5795 1.0877 23 4.4317 2.0533 0.441 6.7253 -0.4676 6.407 0.6798 -0.8624 -0.6299 0.7799 -0.4911 -0.2507 0.2676 -0.3862 -0.1638 0.7106 -0.2588 -0.1037 0.5996 0.0829 0.4493 0.3674 29.8525 5.5808 24 2.613 0.9462 -1.0988 6.273 -3.4638 4.9598 0.6168 -0.6663 -0.5814 0.536 -0.2747 0.1437 1.0563 -0.3884 -0.237 0.9288 -0.3514 -0.2504 0.7429 0.1152 0.6324 -4.1135 22.7577 1.3543 25 7.4754 4.0028 -1.4697 4.2621 -3.2904 3.5259 0.4931 -0.1183 0.3084 0.3966 -0.3287 -0.0118 0.0289 -0.8612 -0.1839 0.6604 -0.1413 -0.1255 0.6225 -0.0684 0.4118 -2.3122 33.1725 -1.2823
Refinement TLS group Show large table (6 x 25) Hide large table ID Refine-ID Refine TLS-ID Selection details Auth asym-ID Auth seq-ID 1 X-RAY DIFFRACTION 1 chain 'A' and (resid 224 through 266 )A224 - 266 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 267 through 294 )A267 - 294 3 X-RAY DIFFRACTION 3 chain 'A' and (resid 295 through 332 )A295 - 332 4 X-RAY DIFFRACTION 4 chain 'A' and (resid 333 through 370 )A333 - 370 5 X-RAY DIFFRACTION 5 chain 'A' and (resid 371 through 455 )A371 - 455 6 X-RAY DIFFRACTION 6 chain 'A' and (resid 456 through 520 )A456 - 520 7 X-RAY DIFFRACTION 7 chain 'A' and (resid 521 through 538 )A521 - 538 8 X-RAY DIFFRACTION 8 chain 'B' and (resid 224 through 266 )B224 - 266 9 X-RAY DIFFRACTION 9 chain 'B' and (resid 267 through 294 )B267 - 294 10 X-RAY DIFFRACTION 10 chain 'B' and (resid 295 through 332 )B295 - 332 11 X-RAY DIFFRACTION 11 chain 'B' and (resid 333 through 370 )B333 - 370 12 X-RAY DIFFRACTION 12 chain 'B' and (resid 371 through 409 )B371 - 409 13 X-RAY DIFFRACTION 13 chain 'B' and (resid 410 through 429 )B