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Minimal 2:2 Ternary Complex between BI-224436 bound HIV-1 Integrase Catalytic Core Domain Dimer and Carboxy Terminal Domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LPU experimental model PDB 3L3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293.15 20 mM Tris pH 7.4, 250-300 mM NaCl, 1 mM DTT, 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.04 59.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.51 α = 90 b = 116.51 β = 103.61 c = 112.8 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2019-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.93 19.85 90.4 0.078 0.09 0.043 0.997 10.8 4.1 48717 53.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.93 3.04 41.1 1.1 1.25 0.59 0.915 1.8 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3L3U 2.93 19.85 39969 4441 90.34 0.22023 0.21569 0.2231 0.26129 0.2712 RANDOM 76.007
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.05 0.12 0.21 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.241 r_long_range_B_refined 13.628 r_long_range_B_other 13.627 r_dihedral_angle_1_deg 7.354 r_scangle_other 6.235 r_mcangle_it 5.554 r_mcangle_other 5.554 r_scbond_it 4.219 r_scbond_other 4.219 r_mcbond_it 3.467
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.241 r_long_range_B_refined 13.628 r_long_range_B_other 13.627 r_dihedral_angle_1_deg 7.354 r_scangle_other 6.235 r_mcangle_it 5.554 r_mcangle_other 5.554 r_scbond_it 4.219 r_scbond_other 4.219 r_mcbond_it 3.467 r_mcbond_other 3.467 r_angle_refined_deg 1.477 r_angle_other_deg 0.473 r_chiral_restr 0.187 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12031 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 368
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing