Software Name Version Classification d*TREKdata scaling PHASERphasing PHENIX(phenix.refine: 1.6_289)refinement XDSdata reduction XDSdata scaling
Refinement Method to determine structure : MOLECULAR REPLACEMENTStarting model : 2HFN; chain AResolution : 2.304→49.925 Å / Isotropic thermal model : overall / σ(F) : 1.99 / Phase error : 25.33 / Stereochemistry target values : TWIN_LSQ_F / Details : twin law "h,-k,-h-l" was used during refinementRfactor Num. reflection % reflection Rfree 0.2155 1900 5.08 % Rwork 0.1645 - - obs 0.1665 37424 94.76 % all - 37424 -
Solvent computation Shrinkage radii : 0.9 Å / VDW probe radii : 1.11 Å / Solvent model : FLAT BULK SOLVENT MODEL / Bsol : 55.928 Å2 / ksol : 0.341 e/Å3 Displacement parameters Baniso -1 Baniso -2 Baniso -3 1- -5.8548 Å2 -0 Å2 0.345 Å2 2- - -6.7286 Å2 0 Å2 3- - - -17.396 Å2
Refinement step Cycle : LAST / Resolution : 2.304→49.925 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 6786 0 186 89 7061
Refine LS restraints Refine-ID Type Dev ideal Number X-RAY DIFFRACTION f_bond_d0.007 7086 X-RAY DIFFRACTION f_angle_d1.241 9636 X-RAY DIFFRACTION f_dihedral_angle_d22.956 2646 X-RAY DIFFRACTION f_chiral_restr0.081 1068 X-RAY DIFFRACTION f_plane_restr0.005 1230
LS refinement shell Resolution (Å)Rfactor Rfree Num. reflection Rfree Rfactor Rwork Num. reflection Rwork Refine-ID % reflection obs (%)2.304-2.3625 0.3407 67 0.3059 1257 X-RAY DIFFRACTION 45 2.3625-2.4264 0.322 122 0.291 2334 X-RAY DIFFRACTION 83 2.4264-2.4978 0.3104 134 0.2784 2529 X-RAY DIFFRACTION 90 2.4978-2.5784 0.3226 141 0.2648 2696 X-RAY DIFFRACTION 95 2.5784-2.6706 0.3191 140 0.2585 2649 X-RAY DIFFRACTION 95 2.6706-2.7775 0.3174 140 0.2578 2665 X-RAY DIFFRACTION 95 2.7775-2.9039 0.3031 141 0.2442 2675 X-RAY DIFFRACTION 95 2.9039-3.0569 0.3051 138 0.2408 2629 X-RAY DIFFRACTION 95 3.0569-3.2484 0.2494 143 0.2068 2709 X-RAY DIFFRACTION 95 3.2484-3.4991 0.2284 140 0.1811 2655 X-RAY DIFFRACTION 95 3.4991-3.8511 0.2107 140 0.1583 2667 X-RAY DIFFRACTION 94 3.8511-4.408 0.1857 140 0.1182 2658 X-RAY DIFFRACTION 95 4.408-5.552 0.1457 142 0.1005 2697 X-RAY DIFFRACTION 95 5.552-45.4641 0.1485 144 0.1061 2729 X-RAY DIFFRACTION 95
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 22) 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 2.1379 -0.6191 1.5978 0.8024 -0.9803 1.6152 0.3142 0.1787 -0.2109 -0.4619 -0.2645 0.0417 0.5562 1.0485 0.0226 0.4512 0.3182 0.0068 0.5721 -0.0705 0.2244 -23.4633 47.4032 -108.0241 2 0.4202 -0.0513 -1.0922 0.0335 0.1325 2.943 -0.2523 0.0007 -0.7228 -0.9981 -0.7071 -0.0495 -0.1524 -0.0759 0.9605 1.5168 0.1627 -0.0052 0.7008 0.0302 1.1772 -25.8033 57.1173 -123.1069 3 0.2574 -0.0586 0.5104 0.71 -0.2357 2.4252 0.305 0.4752 -0.1312 0.2786 -0.0275 -0.0873 -0.6314 0.9026 -0.0461 -0.128 0.2957 0.0177 0.5682 0.046 0.35 -21.7509 53.7485 -106.9829 4 0.5657 -0.0402 0.1423 0.0495 -0.2064 1.285 0.1006 0.1728 -0.065 0.0837 0.1339 -0.0208 1.0633 -0.0439 -0.0395 0.7408 0.3582 -0.0309 0.2006 -0.126 0.2905 -27.031 28.2272 -106.3657 5 2.1444 -0.5617 -0.8625 0.1701 0.1121 1.2744 -0.3862 -0.212 -0.2871 0.2063 0.0723 0.2475 0.866 0.2087 0.1788 0.638 0.1243 0.0802 0.3494 0.0251 0.4374 -23.9702 24.2127 -95.9664 6 0.4009 -0.1751 -0.0398 1.7463 0.3621 0.0747 -0.2078 -0.2748 -0.0858 0.4939 0.5673 0.0382 0.5202 0.3431 -0.3518 0.7105 0.1893 0.0516 0.7366 -0.0504 0.1156 -32.9649 26.5776 -89.653 7 0.6026 -0.4209 -1.2356 1.4961 1.0774 2.7001 0.0877 -0.0282 0.1261 0.2895 -0.2089 0.3952 0.3583 0.4875 0.0481 0.1389 0.0693 0.0675 0.4821 -0.1031 0.2011 -48.9554 55.5251 -76.4551 8 3.9818 0.9305 0.2964 3.1598 -0.138 0.1626 -0.4872 1.0981 0.3255 -0.9002 0.0627 0.1679 0.5321 0.0998 0.3687 0.6534 -0.0286 0.0763 0.6507 0.0899 0.3878 -45.5831 65.6241 -85.883 9 2.7165 1.7617 2.2877 1.7472 0.9719 2.491 -0.0394 0.9193 0.0903 0.1943 0.3705 0.203 0.3283 1.2675 -0.3267 0.3831 0.1467 0.073 0.6903 -0.0416 0.2851 -37.7672 58.5482 -89.0521 10 3.2021 0.2314 -1.5873 0.3302 -0.8989 2.7426 -0.0075 1.2582 -0.1158 0.0569 -0.1487 0.0013 -0.2107 -1.3613 0.012 0.2427 0.1835 0.0901 0.9398 0.0951 0.3027 -40.2266 37.8388 -80.2471 11 0.7671 -0.6833 -0.0993 1.5849 0.4885 1.2289 -0.1654 -0.204 -0.1141 -0.0205 -0.1464 -0.0727 0.617 0.036 -0.1004 0.552 0.2446 -0.0342 0.1396 0.0263 0.0305 -51.4088 32.9083 -71.7438 12 1.851 0.8668 -2.9663 0.4019 -1.5121 6.1044 -0.2089 -0.1806 -0.3015 -1.2145 -0.1339 0.2267 1.9682 0.3427 0.1861 0.9842 0.1384 -0.269 0.2738 0.0002 0.3895 -41.0669 27.3785 -73.1507 13 1.884 1.2896 3.8064 1.3391 2.9989 8.0791 0.5707 -0.2217 -0.2007 0.761 -0.1167 -0.1508 1.2547 -1.1518 -0.5036 0.7635 0.1133 -0.0786 0.574 0.0612 0.2083 -38.0144 29.4929 -60.418 14 0.3582 -0.0987 -0.2016 0.3712 -0.4494 2.4164 0.0755 -0.2863 0.0781 -0.2758 0.0312 -0.1214 -1.3883 1.4485 -0.1203 0.6901 -0.1483 0.0411 0.8186 -0.0472 0.1149 -30.1125 63.1509 -43.9519 15 2.4093 -0.5978 1.0197 1.5063 -1.1443 1.0476 0.0045 0.291 -0.0555 0.6935 0.068 -0.0746 -0.5191 0.3184 0.0059 0.6033 -0.0177 -0.0479 0.7161 -0.1667 0.4067 -25.4367 59.9118 -43.3778 16 5.9847 -0.6663 -2.3374 0.4155 0.0359 1.0571 -0.0143 -0.4246 -0.0743 -0.0702 0.4408 -0.0463 0.0294 -0.9207 -0.3666 0.7163 -0.1904 -0.097 1.0577 0.1812 0.6045 -15.1298 54.6131 -55.3386 17 3.0377 0.1426 -1.4135 0.0788 -0.4564 2.7948 0.3658 -0.2121 0.4149 -0.076 -0.2425 -0.0374 -0.0647 0.0597 -0.3262 0.583 0.0104 0.1442 0.4048 0.0639 0.4356 -32.2972 67.3755 -57.3969 18 1.4292 0.5482 -1.4831 0.5798 -0.8159 1.7125 0.1352 -1.1388 0.2262 0.0608 -0.1458 0.097 0.7868 1.6576 0.0231 1.0694 0.0752 0.1146 1.1496 -0.3748 -0.0647 -39.9106 58.9657 -55.9255 19 0.8428 0.9573 -0.3934 1.7719 -0.9284 0.5541 0.2284 0.1484 0.1388 0.6973 -0.0295 0.1266 0.2783 0.1723 -0.0475 0.9876 -0.0393 0.1323 0.1794 0.0029 0.08 -28.2505 61.8071 -59.3515 20 1.4307 -0.4413 1.9469 0.4257 -0.055 4.7601 0.2016 -0.4075 0.1121 0.1288 -0.023 0.1019 0.2464 -0.9205 -0.2282 0.2616 0.1614 -0.1282 0.9807 -0.0304 0.1595 -26.3817 35.9637 -35.5654 21 0.084 -0.0301 -0.0271 1.2126 -0.1537 0.0509 0.2423 -0.0349 0.0217 -0.4282 -0.3771 0.1364 -0.061 0.7939 0.2632 0.3413 0.1062 -0.0555 0.8045 0.0043 0.2788 -34.4651 34.07 -44.6734 22 0.5948 -0.1122 0.2528 1.2068 -1.8362 4.1034 -0.1813 -0.165 0.0727 0.152 -0.2426 -0.3072 -0.2295 0.2814 0.3982 0.1609 0.0993 -0.0804 0.4855 -0.0291 0.1039 -19.774 35.5965 -43.3466
Refinement TLS group Show large table (4 x 22) Hide large table ID Refine-ID Refine TLS-ID Selection details 1 X-RAY DIFFRACTION 1 (chain A and resid 1:15)2 X-RAY DIFFRACTION 2 (chain A and resid 16:24)3 X-RAY DIFFRACTION 3 (chain A and resid 25:141)4 X-RAY DIFFRACTION 4 (chain B and resid 2:80)5 X-RAY DIFFRACTION 5 (chain B and resid 81:103)6 X-RAY DIFFRACTION 6 (chain B and resid 104:141)7 X-RAY DIFFRACTION 7 (chain C and resid 2:90)8 X-RAY DIFFRACTION 8 (chain C and resid 91:103)9 X-RAY DIFFRACTION 9 (chain C and resid 104:141)10 X-RAY DIFFRACTION 10 (chain D and resid 2:6)11 X-RAY DIFFRACTION 11 (chain D and resid 7:81)12 X-RAY DIFFRACTION 12 (chain D and resid 82:100)13 X-RAY DIFFRACTION 13 (chain D and resid 101:141)14 X-RAY DIFFRACTION 14 (chain E and resid 2:25)15 X-RAY DIFFRACTION 15 (chain E and resid 26:79)16 X-RAY DIFFRACTION 16 (chain E and resid 80:87)17 X-RAY DIFFRACTION 17 (chain E and resid 88:116)18 X-RAY DIFFRACTION 18 (chain E and