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Dissociation of biochemical and antiretroviral activities of Integrase-LEDGF Allosteric Inhibitors revealed by resistance of A125 polymorphic HIV-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 Ammonium sulfate, cacodylate
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.664 α = 90 b = 72.664 β = 90 c = 66.174 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 DECTRIS PILATUS 300K 2016-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 62.93 99 28.4 4.8 13944
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 4LH4 2.35 62.93 8189 492 99.47 0.18711 0.18373 0.1913 0.24367 0.2426 RANDOM 44.248
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] -0.02 -0.01 -0.02 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.867 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 17.41 r_long_range_B_refined 9.051 r_long_range_B_other 8.879 r_scangle_other 6.985 r_dihedral_angle_1_deg 6.335 r_mcangle_it 5.426 r_mcangle_other 5.422 r_scbond_it 4.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.867 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 17.41 r_long_range_B_refined 9.051 r_long_range_B_other 8.879 r_scangle_other 6.985 r_dihedral_angle_1_deg 6.335 r_mcangle_it 5.426 r_mcangle_other 5.422 r_scbond_it 4.56 r_scbond_other 4.483 r_mcbond_other 3.807 r_mcbond_it 3.805 r_angle_refined_deg 2.003 r_angle_other_deg 1.009 r_chiral_restr 0.137 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 1022 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing