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Dual inhibition of HIV-1 replication by Integrase-LEDGF allosteric inhibitors is predominant at post-integration stage during virus production rather than at integration
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LH4 PDB entry 4LH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 1.16-1.36 M ammonium sulfate, 50 mM sodium cacodylate-HCl pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.51 51.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.938 α = 90 b = 72.938 β = 90 c = 65.881 γ = 120
Symmetry Space Group P 31 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 PILATUS 2M 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.19 45.59 97.6 0.029 10071
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.25 93.4 0.123 8.96 3.33 2971
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 PDB entry 4LH4 2.19 45.59 10071 530 99.01 0.18067 0.1777 0.1853 0.23625 0.2356 RANDOM 40.232
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.474 r_dihedral_angle_4_deg 17.494 r_dihedral_angle_3_deg 17.329 r_long_range_B_refined 10.047 r_long_range_B_other 9.932 r_scangle_other 7.24 r_dihedral_angle_1_deg 6.149 r_mcangle_it 5.02 r_mcangle_other 5.018 r_scbond_it 4.843
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.474 r_dihedral_angle_4_deg 17.494 r_dihedral_angle_3_deg 17.329 r_long_range_B_refined 10.047 r_long_range_B_other 9.932 r_scangle_other 7.24 r_dihedral_angle_1_deg 6.149 r_mcangle_it 5.02 r_mcangle_other 5.018 r_scbond_it 4.843 r_scbond_other 4.843 r_mcbond_it 3.505 r_mcbond_other 3.503 r_angle_refined_deg 2.614 r_angle_other_deg 0.868 r_chiral_restr 0.177 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1030 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 31
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction