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HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor BI-224436
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EB2 PDB entry 6EB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1 M sodium cacodylate trihydrate, 0.1 M ammonium sulfate, 10% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.45 49.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.211 α = 90 b = 72.211 β = 90 c = 66.079 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 200K 2018-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 24.3744326678 100 0.05141 0.046 0.012 61 14.6 12002 22.8171075555
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.174 100 0.2756 0.2873 9.04
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 6EB2 2.10002700303 24.3744326678 1.33516230696 11892 2155 95.5225205236 0.22167265269 0.219033887173 0.2198 0.244316687162 0.2446 29.1102107381
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.8311175221 f_angle_d 0.665472641247 f_chiral_restr 0.0453051053364 f_plane_restr 0.00270709876921 f_bond_d 0.0020598760261
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1030 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement HKL-3000 data collection SCALEPACK data scaling HKL-3000 data reduction PHASER phasing