Software Name Version Classification PHENIX1.11.1_2575refinement PDB_EXTRACT3.25 data extraction XSCALEVERSION Jan 26, 2018data scaling XDSVERSION Jan 26, 2018data reduction PHASERphasing
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 6VSSResolution : 2.12→41.52 Å / SU ML : 0.24 / Cross valid method : THROUGHOUT / σ(F) : 1.36 / Phase error : 22.58 Rfactor Num. reflection % reflection Rfree 0.1991 1019 0.44 % Rwork 0.1597 - - obs 0.1599 231541 99.73 %
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 ÅDisplacement parameters Biso max : 148.35 Å2 / Biso mean : 51.8951 Å2 / Biso min : 20.17 Å2 Refinement step Cycle : final / Resolution : 2.12→41.52 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 29519 0 78 1331 30928 Biso mean - - 57.54 49.98 - Num. residues - - - - 3825
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 30190 X-RAY DIFFRACTION f_angle_d0.851 40892 X-RAY DIFFRACTION f_chiral_restr0.052 4612 X-RAY DIFFRACTION f_plane_restr0.005 5418 X-RAY DIFFRACTION f_dihedral_angle_d14.619 18367
LS refinement shell Refine-ID : X-RAY DIFFRACTION / Rfactor Rfree error : 0
Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork % reflection obs (%)2.12-2.23 0.2821 144 0.2475 32449 99 2.23-2.37 0.2141 146 0.2053 32946 100 2.37-2.55 0.2527 145 0.1879 32957 100 2.55-2.81 0.24 146 0.1886 32969 100 2.81-3.21 0.2589 146 0.1855 32973 100 3.22-4.05 0.1968 146 0.1462 33023 100 4.05-41.5 0.1465 146 0.1293 33205 100
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 60) 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 3.0024 -1.6176 0.3735 3.1318 -0.2903 1.761 0.0627 -0.1132 -0.2825 -0.0515 0.0035 -0.1977 0.4775 0.0233 0.0128 0.4587 0.0058 -0.0189 0.2578 0.0433 0.4092 30.6137 58.2758 100.483 2 1.1772 0.5429 0.0017 2.557 -0.6164 2.5954 0.0236 -0.0712 -0.0928 0.0038 -0.0518 -0.247 0.0279 0.2213 0.0353 0.2849 0.0438 0.0239 0.2426 0.0103 0.2941 36.8065 73.7686 98.5258 3 5.311 0.6178 5.6111 0.654 1.1747 9.1876 -0.3654 0.0668 0.6837 -0.0148 -0.2176 0.098 -1.0107 -0.3934 0.6078 0.6128 0.117 0.0677 0.3179 0.035 0.5171 16.7711 109.4135 66.497 4 1.6258 0.4445 0.5849 1.5058 0.9469 3.387 0.0338 -0.1852 0.1676 0.1541 -0.1434 0.1559 -0.263 -0.2932 0.1211 0.3213 0.031 0.0392 0.2405 -0.0164 0.3811 26.7562 94.7552 76.3532 5 3.5114 -0.4128 1.9777 1.1634 1.4455 6.0698 0.1574 0.378 0.0952 -0.3747 -0.0516 0.2148 -0.6991 -0.1828 -0.0568 0.4937 0.1348 0.0403 0.3191 0.0621 0.4863 21.6711 102.7967 59.2473 6 1.51 -0.3856 -0.3781 2.4522 -0.1056 1.8195 0.0586 0.0582 0.2576 -0.1162 0.001 -0.3211 -0.3217 0.2184 -0.0541 0.2514 -0.0328 0.0264 0.2206 0.0025 0.3443 39.2434 92.8666 66.5019 7 1.5715 0.5273 -0.8314 2.9091 0.2061 2.6661 -0.1731 0.0107 -0.3406 -0.194 0.1088 -0.0081 0.5209 -0.0278 0.1008 0.3004 0.0548 0.021 0.244 -0.0137 0.3982 40.2163 50.5841 47.9168 8 1.4027 0.1848 -0.7099 2.6287 -0.1737 2.1995 0.0876 0.0414 0.0672 -0.1563 -0.0228 0.091 -0.2294 -0.0615 -0.102 0.2665 0.0172 0.0031 0.2972 -0.0068 0.3275 39.6444 68.3468 52.5068 9 4.5501 3.282 -0.5514 6.249 -1.208 3.6775 0.1595 0.1041 -0.4479 0.059 -0.0207 -0.201 0.8011 -0.0015 -0.0295 0.5198 0.0679 -0.0013 0.2412 -0.047 0.4346 40.1374 44.6015 53.0016 10 2.7751 -0.7008 1.0245 2.3006 1.6299 2.8677 0.051 -0.3815 -0.5972 0.5491 0.1315 -0.1253 1.0519 0.4106 -0.1274 0.5068 0.1531 -0.0286 0.4078 0.0513 0.5878 50.9133 51.3557 65.9143 11 5.153 2.3727 -3.2838 2.784 0.3497 4.3602 0.0668 -0.7837 0.0703 0.2918 0.2761 -0.1754 0.1646 0.8995 -0.3859 0.2799 0.1253 -0.0988 0.7037 -0.0291 0.5512 57.1374 65.893 75.8686 12 1.69 0.1043 -0.3531 2.2456 0.3381 3.277 -0.0368 -0.1424 -0.0896 0.0476 0.0859 -0.1573 0.0357 0.2403 -0.0194 0.162 0.0515 -0.021 0.2455 -0.0003 0.3423 45.5444 65.1799 64.3955 13 9.1425 -6.2947 0.5561 4.431 0.1551 2.1869 -0.3051 -0.796 -0.1764 0.4138 0.401 -0.0189 0.5707 -0.2498 -0.0917 0.5895 -0.1028 0.0384 0.3929 0.1264 0.4544 16.7191 50.4376 108.0239 14 3.2328 -0.6386 0.0023 3.6094 0.49 2.748 0.1474 -0.2362 -0.0627 -0.143 0.0108 -0.0933 0.094 -0.3819 -0.1331 0.3436 -0.0558 0.0148 0.3572 0.0639 0.3342 10.3179 60.1014 90.5219 15 1.3996 0.4759 0.6899 1.6186 0.4237 2.2542 0.1956 -0.1908 -0.4245 0.2154 0.012 0.0275 0.6036 -0.3867 -0.1598 0.5266 -0.1407 -0.008 0.4009 0.1271 0.4875 8.7708 46.2174 92.7996 16 2.4891 1.0757 -0.3704 6.9663 -1.1461 4.6538 0.1416 0.1267 -0.6676 -0.6682 -0.1457 -0.1741 0.9007 -0.5861 -0.0297 0.6133 -0.1874 -0.0709 0.4288 0.0085 0.6341 3.5807 38.5603 75.0359 17 8.4934 0.5973 -1.6165 1.9145 -0.2329 4.6165 -0.0902 0.6153 0.4086 0.0422 -0.035 0.2534 0.0918 -1.09 0.1085 0.5816 -0.1315 -0.1235 0.7715 0.059 0.7255 -6.1937 48.6071 72.362 18 1.9918 1.1266 -2.0218 8.211 -4.4696 3.5204 0.4102 -0.0136 -0.5931 0.182 -0.1535 0.7472 0.2034 -1.0735 -0.1438 0.5546 -0.2451 -0.011 0.6685 0.0536 0.5315 -2.6481 47.7624 86.9809 19 2.0939 -0.6081 0.9323 1.6209 0.7422 3.3553 -0.0411 -0.0772 -0.1748 -0.2499 0.0332 0.1316 0.0051 -0.4246 -0.0027 0.4461 0.0012 0.0175 0.3354 0.0599 0.4104 5.3291 58.6695 82.0654 20 4.9183 3.3034 4.9736 5.3157 4.9303 8.5095 -0.1975 0.0906 0.7302 0.0001 -0.0276 0.3757 -0.8595 -0.0608 0.3493 0.4919 0.1392 0.0967 0.34 0.0569 0.5916 7.2388 106.8438 67.775 21 1.4723 0.2905 0.5421 1.4455 0.2065 3.9116 0.0684 0.1577 0.2339 -0.1875 -0.0893 0.0848 0.0389 0.0301 0.0146 0.2743 0.0707 -0.0122 0.415 0.0437 0.4416 6.0911 87.06 62.4807 22 1.7522 0.2854 -0.29 2.1757 -0.2191 1.4359 0.2161 -0.1571 0.3539 0.2816 -0.0037 0.4475 -0.2691 -0.2986 -0.1724 0.2646 0.092 0.0633 0.4425 -0.0147 0.5244 -3.9409 90.3658 78.1312 23 2.3327 0.0472 0.6014 2.2568 -0.1424 2.5774 -0.0221 -0.0093 -0.336 0.0193 0.173 0.579 -0.0123 -0.4252 -0.053 0.2425 -0.0474 -0.0198 0.5936 0.0147 0.648 -12.8799 69.9867 73.4046 24 1.3487 -1.1613 -0.5188 2.4246 -0.0345 1.2929 0.1727 0.3004 0.1653 -0.1406 -0.0487 0.7029 0.0572 -0.5207 -0.0951 0.2156 0.065 -0.0033 0.5874 0.0712 0.6301 -10.1978 84.0675 69.26 25 1.5071 0.6028 -0.4029 2.5512 -0.1876 2.0387 -0.0003 0.0537 0.0552 -0.1182 0.0249 0.1468 0.0169 -0.2524 -0.0214 0.199 0.0299 -0.0138 0.3869 0.0077 0.3861 2.0161 77.7075 67.3478 26 7.7061 4.5632 -5.6112 4.0772 -5.2873 7.2947 -0.3398 0.2482 -0.5282 -0.4124 0.0244 -0.304 0.3867 -0.2436 0.2811 0.4381 0.0062 -0.0079 0.2359 -0.0857 0.3353 30.9659 48.2554 39.0007 27 2.9437 0.7936 -0.1204 6.6056 -0.5548 1.833 -0.1509 0.0292 -0.5694 0.4539 0.0745 -0.0272 0.2832 -0.2373 0.0746 0.2956 -0.0241 0.0329 0.267 -0.034 0.4062 18.5441 49.6678 55.4052 28 3.1707 -0.7103 -0.6756 2.2644 0.3998 1.8759 0.0327 0.6532 -0.2046 -0.2666 -0.0704 0.1567 0.0723 -0.4024 0.0208 0.2822 -0.0238 -0.0577 0.4323 -0.0527 0.3066 14.9922 58.1456 40.3267 29 3.0087 -1.0323 -0.2528 2.4039 0.8796 2.8364 -0.184 0.2434 -0.4164 0.1468 -0.0264 0.5288 0.1101 -0.6113 0.1633 0.2611 -0.0434 0.0361 0.4218 -0.0091 0.4253 4.754 58.7901 53.1887 30 5.9026 -5.0738 -0.2027 8.8118 -1.102 1.0744 -0.288 -0.6363 0.188 0.3457 0.3702 -0.036 -0.3279 0.249 -0.1102 0.524 -0.0544 -0.0208 0.4915 -0.14 0.308 56.2141 34.6399 35.1979 31 2.5817 0.1501 0.8006 2.5531 -0.0549 2.8445 0.1367 -0.2964 0.0047 0.0046 0.0158 -0.1681 0.196 0.5417 -0.1559 0.3601 -0.0432 -0.0208 0.5763 -0.0664 0.3183 67.2165 23.7719 21.7051 32 1.5487 -0.1839 -0.8602 1.8826 -0.1404 2.3319 0.0363 -0.1523 0.3404 0.1598 0.1014 -0.0133 -0.502 0.5487 -0.1016 0.4802 -0.154 0.0029 0.4549 -0.1359 0.3991 63.2293 38.6626 25.9768 33 1.494 0.5441 -0.4547 2.4982 0.2174 2.9973 -0.0513 0.0148 0.3047 -0.3016 0.2156 -0.2867 -0.3555 0.8512 -0.1523 0.4439 -0.1877 0.0333 0.6299 -0.1179 0.4202 73.9972 35.4697 10.9118 34 4.8222 3.7419 3.7657 8.4909 6.2081 6.7481 -0.2677 0.1633 0.3918 -0.5972 -0.0859 0.3618 -0.5116 0.3282 0.3821 1.0825 -0.1518 0.0221 0.3881 0.0538 0.4065 53.2741 36.7257 -34.8303 35 2.0695 0.6991 -0.2343 5.3062 -0.1269 0.677 -0.1946 -0.0025 0.4659 0.1299 0.1417 -0.0006 -0.5518 0.479 0.0643 0.8183 -0.2589 0.0072 0.4535 -0.0249 0.476 62.928 35.0621 -16.5754 36 2.1877 -0.9499 0.3436 2.1998 -0.0601 2.3516 -0.1339 0.1715 0.309 -0.2465 0.1875 -0.3873 -0.4644 0.8994 -0.0124 0.6519 -0.3126 0.0948 0.6746 -0.0979 0.4399 73.2272 25.9675 -22.8551 37 5.9414 2.4589 -4.9732 3.0401 -1.325 8.1433 -0.5249 0.0411 -1.1677 0.0012 -0.0821 -0.5944 1.3109 0.2989 0.6673 0.9812 0.3419 -0.0632 0.5404 -0.0645 0.664 71.6765 -21.9791 -3.619 38 2.7338 0.4837 -1.1261 1.9657 0.0291 4.0351 0.0546 0.1466 -0.2081 -0.2002 0.1512 -0.2801 0.2118 0.5316 -0.2049 0.5051 0.1586 -0.0243 0.6137 -0.1465 0.398 73.4763 -2.4684 -7.73 39 3.9405 2.1993 -2.9794 1.5165 -0.596 6.4434 -0.1149 -0.2629 -0.6314 0.1871 0.0159 -0.0453 1.3204 0.6972 0.098 0.9284 0.3302 -0.1474 0.6061 -0.0383 0.5397 71.56 -16.2564 6.1287 40 1.4272 0.287 0.3621 2.6375 0.5898 1.6611 0.0171 -0.2607 -0.1915 0.2681 0.2169 -0.6495 0.3946 0.9471 -0.1861 0.4642 0.2262 -0.0784 0.9536 -0.1206 0.5281 83.9805 2.0658 7.1968 41 2.1827 -1.6073 -2.2316 3.2195 1.4472 2.7834 -0.2269 -0.1891 0.06 0.0123 0.2381 -0.2124 0.2677 0.5757 -0.006 0.4966 0.0649 -0.0363 0.573 -0.0583 0.404 74.0384 3.1586 -1.054 42 7.5057 -3.159 -3.4905 5.6916 2.9988 5.7485 0.0372 -0.0546 -0.0652 -0.1921 0.3445 -0.6385 0.4116 1.0705 -0.3628 0.4469 0.0752 0.0121 0.7119 -0.127 0.4213 78.9094 2.9217 -8.3488 43 3.8763 -5.6087 2.8363 9.2367 -3.7422 4.8461 -0.5337 -0.7405 0.1105 0.6567 0.4032 -0.0303 -0.568 0.218 0.1293 0.4621 -0.0292 0.0227 0.4367 -0.0741 0.3873 48.5019 29.0845 37.581 44 4.107 -1.6533 -0.4914 4.1456 0.5739 2.0504 -0.0154 0.1316 0.5375 -0.722 0.0263 0.164 -0.2923 0.0316 -0.0132 0.4732 -0.0502 -0.1026 0.2538 -0.0208 0.3869 43.2528 23.2343 18.094 45 5.1786 -1.6566 1.3469 4.8938 -0.4143 2.6005 -0.2112 0.1995 0.508 -0.0332 0.0108 -0.0774 -0.5396 0.3766 0.0719 0.4029 -0.0313 -0.0107 0.3295 -0.0816 0.3371 45.113 26.4919 25.8504 46 3.2927 -0.0338 -0.7704 4.2551 0.5496 3.6388 0.0625 -0.4011 0.1606 0.1654 -0.047 0.1402 -0.106 0.0467 -0.0042 0.3212 -0.0126 -0.0014 0.2524 -0.0459 0.2674 40.7622 18.9192 33.2419 47 1.3627 0.5831 0.0142 3.5015 0.8564 3.9165 -0.0297 0.0095 -0.0461 -0.2016 -0.0907 0.3263 0.5417 -0.2419 0.159 0.43 -0.0539 -0.0392 0.2852 -0.0042 0.3307 33.8537 4.4791 23.6395 48 1.4193 0.2805 -0.1127 3.12 0.8855 2.5949 -0.1836 0.1469 0.1987 -0.9154 0.0177 0.4206 -0.1687 -0.1567 0.1145 0.5817 0.0026 -0.1471 0.2662 0.0121 0.3715 37.9666 16.4965 13.1563 49 4.0216 3.1698 1.4658 4.2217 2.4623 2.9496 -0.4216 0.3678 0.5037 -0.8692 0.5752 0.4578 -0.9511 0.3213 -0.0907 1.0654 -0.0187 -0.0753 0.3799 0.103 0.4425 43.8414 37.5446 -32.8673 50 2.7728 -0.0757 0.2619 2.3583 0.3759 4.43 -0.0342 -0.0658 0.2841 -0.2346 0.2241 -0.1699 -0.8732 0.1427 0.0497 0.665 0.0045 -0.0609 0.269 -0.0077 0.4506 40.2825 29.6233 -17.8049 51 2.7893 0.4024 0.1899 2.48 0.4469 3.98 -0.1419 0.0313 -0.0791 -0.4192 0.1414 -0.0874 0.2972 0.088 -0.0028 0.625 -0.032 -0.0222 0.3152 0.0064 0.3148 44.2033 16.2803 -19.169 52 2.5268 1.0288 0.1146 2.7269 0.2145 3.4278 -0.1413 0.1213 0.1009 -0.6696 0.0813 -0.2029 -0.6265 0.1592 -0.0202 0.6539 -0.0194 -0.0797 0.2999 0.0592 0.3649 42.9811 27.9789 -24.9907 53 1.1484 0.5355 -0.6475 1.813 -0.5396 1.7181 0.0933 0.1761 0.5466 -0.4595 0.0665 0.2379 -1.0948 -0.5685 -0.1266 0.9427 0.1472 -0.0928 0.3564 0.0611 0.5413 34.1628 35.0226 -23.2573 54 2.3821 -0.0694 -0.418 2.5611 -0.7043 3.7899 0.1674 -0.1541 0.8234 0.1195 0.0105 0.2732 -1.1479 -0.3737 -0.1838 0.8019 0.1833 0.0025 0.4588 -0.0509 0.6765 27.4404 34.8789 -6.4703 55 3.9902 -0.124 -0.4813 4.9459 -0.7818 6.3857 -0.2095 -0.2958 0.1385 0.3437 0.1746 0.3956 -0.0811 -1.3508 0.1146 0.462 0.0698 -0.0052 0.6774 -0.015 0.6194 21.0712 18.9988 -2.336 56 1.7999 -0.4819 -1.0679 4.1533 -1.3931 5.3906 -0.3681 0.1432 0.2955 -0.3069 0.2641 0.3621 -0.2473 -0.82 0.1038 0.5465 0.0964 -0.0862 0.4032 -0.0109 0.4352 24.9543 25.4552 -15.5583 57 2.3391 0.6325 -0.1376 1.5709 0.4944 3.7294 -0.1119 -0.1062 0.1815 -0.1375 0.0052 0.1603 -0.0823 -0.1502 0.1119 0.5019 0.0296 -0.0458 0.2583 -0.033 0.3839 36.5887 18.8497 -11.2884 58 1.3646 -0.0927 -0.454 0.1082 0.5784 1.9633 -0.1529 -0.0335 -0.3013 0.2987 0.1111 0.0425 0.6735 0.3109 0.0684 0.8104 0.0719 0.0029 0.331 0.011 0.3913 56.0931 -15.1062 -2.4624 59 2.2974 -0.0001 -1.7138 1.4889 -0.5085 3.7959 -0.1671 -0.4142 -0.0751 0.149 0.0365 -0.1042 0.7758 0.6811 0.1574 0.8009 0.1225 0.0199 0.3369 0.009 0.4011 55.4538 -14.6792 -1.1538 60 1.1869 -0.4522 0.1765 2.0245 0.2667 2.2927 -0.0387 0.1101 -0.2693 -0.1259 0.0112 0.2512 0.6782 -0.1909 0.0282 0.6784 -0.1108 0.0077 0.2806 -0.0148 0.3379 40.9538 -8.5926 -9.4265
Refinement TLS group Show large table (6 x 60) 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 22 through 116 )A22 - 116 2 X-RAY DIFFRACTION 2 chain 'A' and (resid 117 through 338 )A117 - 338 3 X-RAY DIFFRACTION 3 chain 'B' and (resid 21 through 54 )B21 - 54 4 X-RAY DIFFRACTION 4 chain 'B' and (resid 55 through 116 )B55 - 116 5 X-RAY DIFFRACTION 5 chain 'B' and (resid 117 through 143 )B117 - 143 6 X-RAY DIFFRACTION 6 chain 'B' and (resid 144 through 338 )B144 - 338 7 X-RAY DIFFRACTION 7 chain 'C' and (resid 21 through 76 )C21 - 76 8 X-RAY DIFFRACTION 8 chain 'C' and (resid 77 through 116 )C77 - 116 9 X-RAY DIFFRACTION 9 chain 'C' and (resid 117 through 143 )C117 - 143 10 X-RAY DIFFRACTION 10 chain 'C' and (resid 144 through 232 )C144 - 232 11 X-RAY DIFFRACTION 11 chain 'C' and (resid 233 through 251 )C233 - 251 12 X-RAY DIFFRACTION 12 chain 'C' and (resid 252 through 338 )C252 - 338 13 X-RAY DIFFRACTION 13 chain 'D' and (resid 19 through 54 )D