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Crystal Structure of HIV-1 Reverse Transcriptase (K103N, Y181C) variant in complex with (E)-3-(3-chloro-5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)phenyl)acrylonitrile (JLJ532), a non-nucleoside inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H4M PDB Code: 4H4M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 18% (w/v) PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 5 mM spermine, and 50 mM citric acid, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.8 56.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.953 α = 90 b = 73.874 β = 99.87 c = 108.457 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 77 CCD ADSC QUANTUM 315 Monochrometer 2013-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.01 50 99.6 0.122 32.2 3.7 25032 25032 -3 85.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.01 3.06 100 0.488 3.8 1261
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 FOURIER SYNTHESIS Rfree Flag PDB Code: 4H4M 3.014 34.965 1.34 25024 25024 2000 99.38 0.2319 0.2289 0.2287 0.2657 0.267 Random 60.8217
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 12.477 f_angle_d 0.724 f_chiral_restr 0.054 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7715 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 29
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling