Software Name Version Classification REFMAC5.3.0037refinement ADSCQuantumdata collection DENZOdata reduction SCALEPACKdata scaling REFMAC5.3 phasing
Refinement Method to determine structure : FOURIER SYNTHESISStarting model : PDB entry 2G8QResolution : 1.58→30 Å / Cor.coef. Fo :Fc : 0.955 / Cor.coef. Fo :Fc free : 0.934 / SU B : 3.315 / SU ML : 0.063 / TLS residual ADP flag : LIKELY RESIDUAL / Cross valid method : THROUGHOUT / ESU R : 0.101 / ESU R Free : 0.103 / Stereochemistry target values : MAXIMUM LIKELIHOOD / Details : HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONSRfactor Num. reflection % reflection Selection details Rfree 0.22678 1574 5.1 % RANDOM Rwork 0.18592 - - - obs 0.18793 29500 94.48 % -
Solvent computation Ion probe radii : 0.8 Å / Shrinkage radii : 0.8 Å / VDW probe radii : 1.4 Å / Solvent model : MASKDisplacement parameters Biso mean : 15.397 Å2 Baniso -1 Baniso -2 Baniso -3 1- -0.12 Å2 0 Å2 -0.1 Å2 2- - -0.35 Å2 0 Å2 3- - - 0.47 Å2
Refine analyze Free Obs Luzzati coordinate error 0.103 Å 0.101 Å
Refinement step Cycle : LAST / Resolution : 1.58→30 ÅProtein Nucleic acid Ligand Solvent Total Num. atoms 1902 0 22 313 2237
Refine LS restraints Show large table (5 x 33) Hide large table Refine-ID Type Dev ideal Dev ideal target Number X-RAY DIFFRACTION r_bond_refined_d0.009 0.021 1979 X-RAY DIFFRACTION r_bond_other_dX-RAY DIFFRACTION r_angle_refined_deg1.155 1.937 2680 X-RAY DIFFRACTION r_angle_other_degX-RAY DIFFRACTION r_dihedral_angle_1_deg5.76 5 246 X-RAY DIFFRACTION r_dihedral_angle_2_deg35.563 25.222 90 X-RAY DIFFRACTION r_dihedral_angle_3_deg10.926 15 340 X-RAY DIFFRACTION r_dihedral_angle_4_deg12.304 15 8 X-RAY DIFFRACTION r_chiral_restr0.074 0.2 297 X-RAY DIFFRACTION r_gen_planes_refined0.004 0.02 1485 X-RAY DIFFRACTION r_gen_planes_otherX-RAY DIFFRACTION r_nbd_refined0.182 0.2 905 X-RAY DIFFRACTION r_nbd_otherX-RAY DIFFRACTION r_nbtor_refined0.294 0.2 1355 X-RAY DIFFRACTION r_nbtor_otherX-RAY DIFFRACTION r_xyhbond_nbd_refined0.128 0.2 239 X-RAY DIFFRACTION r_xyhbond_nbd_otherX-RAY DIFFRACTION r_metal_ion_refinedX-RAY DIFFRACTION r_metal_ion_otherX-RAY DIFFRACTION r_symmetry_vdw_refined0.189 0.2 51 X-RAY DIFFRACTION r_symmetry_vdw_otherX-RAY DIFFRACTION r_symmetry_hbond_refined0.121 0.2 36 X-RAY DIFFRACTION r_symmetry_hbond_otherX-RAY DIFFRACTION r_symmetry_metal_ion_refinedX-RAY DIFFRACTION r_symmetry_metal_ion_otherX-RAY DIFFRACTION r_mcbond_it0.546 1.5 1277 X-RAY DIFFRACTION r_mcbond_otherX-RAY DIFFRACTION r_mcangle_it0.882 2 2015 X-RAY DIFFRACTION r_scbond_it1.299 3 785 X-RAY DIFFRACTION r_scangle_it2.053 4.5 665 X-RAY DIFFRACTION r_rigid_bond_restrX-RAY DIFFRACTION r_sphericity_freeX-RAY DIFFRACTION r_sphericity_bonded
LS refinement shell Resolution : 1.58→1.622 Å / Total num. of bins used : 20 Rfactor Num. reflection % reflection Rfree 0.289 121 - Rwork 0.231 2043 - obs - - 90.73 %
Refinement TLS params. Method : refined / Refine-ID : X-RAY DIFFRACTION
Show large table (25 x 20) 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 12.5682 -1.4086 -1.1011 1.6192 1.5838 10.8036 0.1855 -0.1401 1.081 -0.4798 0.3336 -0.2135 -1.9224 0.5689 -0.5192 0.3057 -0.1196 0.098 -0.0444 -0.01 0.0027 33.1809 15.1904 12.2192 2 3.9 -0.1235 0.8219 3.6313 1.0334 7.2049 0.0794 0.1737 0.0169 -0.0733 0.0323 -0.1054 -0.2574 0.0245 -0.1116 0.0652 -0.0078 0.0249 0.0387 0.0205 -0.0142 30.0018 5.914 8.2966 3 12.913 -11.829 -16.7712 24.1925 13.1393 22.1524 -0.5688 0.458 -0.954 0.8573 -0.6747 1.4098 1.058 -1.1129 1.2435 0.0431 0.0185 -0.0726 0.2454 -0.1605 0.0452 24.3663 -4.1723 -1.3673 4 4.2811 1.2004 -0.9277 12.3091 5.5707 5.8523 0.1087 0.638 -0.1278 -0.6964 -0.0934 0.1875 -0.336 -0.2902 -0.0153 0.0467 -0.0069 0.0244 0.1246 -0.0313 -0.0704 33.7692 0.1388 -2.9365 5 9.9091 -4.2327 -4.3309 4.7863 0.8653 2.2185 0.1231 -0.3456 0.8562 -0.237 0.1954 -0.8844 -0.3738 0.4217 -0.3186 0.0401 -0.0854 0.0779 0.0454 -0.0662 0.0401 41.0198 5.1513 2.9816 6 1.8189 0.258 -0.772 0.5444 -0.6421 3.7844 -0.0551 0.0736 -0.0424 -0.09 0.0627 -0.0061 -0.0121 -0.1554 -0.0077 0.0333 0.0005 -0.0014 0.0388 0.0106 0.0196 25.1418 0.8113 13.1519 7 5.1172 0.8023 1.1738 1.3987 -0.3243 2.6624 -0.0289 -0.0456 -0.1296 0.0143 0.0005 -0.1267 -0.1031 -0.0814 0.0284 0.0379 0.0044 0.0056 0.0379 0.0071 0.0324 30.1296 -1.656 24.2737 8 11.4915 1.9027 -6.2447 0.4241 -1.2679 5.1535 -0.3429 0.0741 -0.5972 -0.2014 0.08 -0.3133 0.465 0.2481 0.263 0.058 -0.0071 0.0753 0.0173 -0.0499 0.0519 38.3938 -4.7162 2.1366 9 6.8394 2.6603 -6.0614 1.1318 -2.0745 6.1986 -0.4546 0.0654 -0.5063 -0.2669 0.1828 -0.2589 0.6484 -0.0337 0.2718 0.0902 -0.0247 0.0436 0.0098 -0.0546 0.0156 31.4312 -8.4603 3.8012 10 1.9007 0.1158 0.1637 2.8244 0.3644 2.4279 -0.0566 -0.0267 0.048 -0.065 0.0583 -0.0665 -0.0377 -0.1738 -0.0017 0.0419 0.0053 0.0041 0.0451 0.0078 0.0205 29.3107 2.6403 18.8823 11 4.1254 0.1068 1.4858 2.9086 0.2561 4.5078 0.0006 0.2089 -0.172 0.09 0.169 -0.1059 0.1466 0.1011 -0.1696 0.0118 -0.0046 0.0122 0.0545 -0.0103 0.0386 16.2359 -4.9029 30.3931 12 30.1823 -27.9274 16.7571 25.8411 -15.5052 9.3035 0.7327 1.3245 -1.9534 0.4056 0.2275 0.9852 -1.0434 1.0249 -0.9602 -0.0187 0.0132 0.0729 0.3208 0.0683 0.5355 10.9958 10.7944 21.9112 13 0.546 -2.3545 0.4503 15.2211 2.1047 3.6025 0.2125 0.3895 0.0267 -1.2112 -0.2845 -0.0461 -0.1565 0.4853 0.072 0.104 0.0061 -0.0295 0.141 0.0618 -0.0951 8.7258 1.593 18.359 14 15.7157 2.1294 3.5959 10.0551 0.884 2.9992 0.2369 0.6493 -1.2549 -0.7639 -0.3362 0.2459 0.285 0.0329 0.0993 0.0422 0.0104 0.0217 0.0706 -0.0788 0.0167 9.6565 -8.3087 20.6295 15 2.3642 0.2423 1.3242 1.4717 1.1456 1.8688 -0.0731 0.1507 0.0702 -0.1469 0.0181 0.0512 -0.0496 0.0412 0.055 0.0285 -0.0087 0.0056 0.0337 0.0125 0.0461 12.5 2.4964 32.5061 16 7.0228 5.4598 0.6714 8.7976 2.4153 1.1656 -0.0517 -0.2029 -0.2044 0.1623 0.0285 0.3698 0.2095 -0.0872 0.0232 0.0157 -0.0062 0.0011 0.0276 0.0388 0.0529 8.0283 -2.3759 46.7441 17 0.7663 0.6285 -0.1359 0.8675 0.5201 1.1572 -0.0326 0.0038 0.0791 -0.0936 -0.0586 0.0869 -0.0665 -0.0552 0.0912 0.0218 0.0067 -0.0241 0.0279 0.0134 0.054 9.5161 5.7751 39.6 18 4.1863 -2.1954 0.0206 2.9147 1.6542 7.7265 -0.0041 0.7446 -0.5438 -0.5591 -0.3725 0.4999 0.2883 -0.3847 0.3766 0.0644 0.0043 -0.0545 0.0359 -0.0973 0.0429 -1.0141 -4.9203 17.8033 19 0.8301 0.2054 0.3698 0.9483 0.5841 1.2493 -0.0927 0.0963 0.1325 -0.1811 -0.002 0.1683 -0.2537 -0.129 0.0947 0.0518 0.0077 -0.0449 0.0338 0.0232 0.0654 5.5672 5.2163 32.0645 20 5.7105 -1.8322 1.0615 2.6605 -0.6981 2.8314 0.0445 0.0364 -0.1908 -0.0734 -0.025 0.1102 0.107 0.072 -0.0194 0.0388 -0.0238 0.0021 0.0275 0.0131 0.0422 13.5757 -3.1253 40.1399
Refinement TLS group Show large table (7 x 20) Hide large table ID Refine-ID Refine TLS-ID Auth asym-ID Label asym-ID Auth seq-ID Label seq-ID 1 X-RAY DIFFRACTION 1 AA1 - 6 1 - 6 2 X-RAY DIFFRACTION 2 AA7 - 15 7 - 15 3 X-RAY DIFFRACTION 3 AA16 - 23 16 - 23 4 X-RAY DIFFRACTION 4 AA24 - 32 24 - 32 5 X-RAY DIFFRACTION 5 AA33 - 41 33 - 41 6 X-RAY DIFFRACTION 6 AA42 - 61 42 - 61 7 X-RAY DIFFRACTION 7 AA62 - 77 62 - 77 8 X-RAY DIFFRACTION 8 AA78 - 95 78 - 95 9 X-RAY DIFFRACTION 9 AA96 - 104 96 - 104 10 X-RAY DIFFRACTION 10 AA105 - 124 105 - 124 11 X-RAY DIFFRACTION 11 BB1 - 15 1 - 15 12 X-RAY DIFFRACTION 12 BB16 - 23 16 - 23 13 X-RAY DIFFRACTION 13 BB24 - 31 24 - 31 14 X-RAY DIFFRACTION 14 BB32 - 39 32 - 39 15 X-RAY DIFFRACTION 15 BB40 - 58 40 - 58 16 X-RAY DIFFRACTION 16 BB59 - 70 59 - 70 17 X-RAY DIFFRACTION 17 BB71 - 83 71 - 83 18 X-RAY DIFFRACTION 18 BB84 - 96 84 - 96 19 X-RAY DIFFRACTION 19 BB97 - 110 97 - 110 20 X-RAY DIFFRACTION 20 BB111 - 124 111 - 124