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D30N mutant HIV protease in complex with benzoxaborolone analog of darunavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 278 100 mM Tris pH 7.5 and 500 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.74 55.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.44 α = 90 b = 86.38 β = 90 c = 46.34 γ = 90
Symmetry Space Group P 21 21 2
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 6M 2018-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.96862 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.35 48.4 99.9 0.075 0.999 15.7 12.3 52315 18.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.39 99 1.527 0.65 1.33
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 6c8x 1.35 48.4 1.35 52258 2000 99.89 0.1981 0.1972 0.1982 0.2212 0.2203 23.07
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 14.8004 f_angle_d 1.2336 f_chiral_restr 0.0871 f_bond_d 0.0122 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1503 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing