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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 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.363 α = 90 b = 72.363 β = 90 c = 65.819 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 2M 2013-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 1.9 38.18 88.7 12.37 3.3 26873
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 2.3 36.18 8663 456 99.29 0.19635 0.19244 0.1963 0.27197 0.2781 RANDOM 47.516
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 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.842 r_dihedral_angle_3_deg 19.925 r_dihedral_angle_4_deg 18.814 r_long_range_B_other 13.727 r_long_range_B_refined 13.698 r_scangle_other 8.204 r_mcangle_it 6.087 r_mcangle_other 6.084 r_dihedral_angle_1_deg 5.835 r_scbond_it 5.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.842 r_dihedral_angle_3_deg 19.925 r_dihedral_angle_4_deg 18.814 r_long_range_B_other 13.727 r_long_range_B_refined 13.698 r_scangle_other 8.204 r_mcangle_it 6.087 r_mcangle_other 6.084 r_dihedral_angle_1_deg 5.835 r_scbond_it 5.308 r_scbond_other 5.303 r_mcbond_it 4.214 r_mcbond_other 4.212 r_angle_refined_deg 1.682 r_angle_other_deg 1.019 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 1023 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing