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Crystal Structure of HIV-1 K103N, Y181C mutant Reverse Transcriptase in Complex with 5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-7-fluoro-2-naphthonitrile (JLJ635), a Non-nucleoside Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 0 mM MES pH 6.0, 18% PEG 8,000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, and 5 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.74 α = 90 b = 74.17 β = 99.369 c = 108.6 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 16M 2015-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2.79 50 99.3 0.073 0.084 0.995 14.51 3.75 31556 74.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.87 93.2 0.571 0.672 0.813 2.62 3.5
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 6OE3 2.79 48.26 0.69 31547 1577 99.34 0.2403 0.2385 0.2423 0.275 0.2749 88.75
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 14.8937 f_angle_d 0.9713 f_chiral_restr 0.0393 f_bond_d 0.0041 f_plane_restr 0.0037
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7511 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing