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Crystal Structure of HIV-1 Reverse Transcriptase in Complex with 5-(2-(2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy)phenoxy)-2-naphthonitrile (JLJ600)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MFB PDB Code:4MFB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 18% w/v PEG 8000, 100 mM ammonium sulfate, 15 mM magnesium sulfate, 50 mM Imidazole (pH 6.5), and 5 mM spermine-HCl
Crystal Properties Matthews coefficient Solvent content 3.16 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 220.271 α = 90 b = 67.218 β = 108.08 c = 102.483 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 80 CCD ADSC QUANTUM 315r 2013-10-18 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 2.49 50 98.9 0.065 15.7 3.7 181376 49497 -3 50.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.53 89.7 0.373 2.97 3.1 2197
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE PDB Code:4MFB 2.491 38.765 1.35 49465 1999 98.53 0.2402 0.2383 0.2447 0.2866 0.2876 Random selection 60.6
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 14.418 f_angle_d 0.858 f_chiral_restr 0.033 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7665 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling