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Wild-type HIV-1 protease in complex with a phenylboronic acid (P2') analog of darunavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NU3 PDB entry 3NU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 2.0 mg/mL protease, 1.5 mg/mL ligand, 10% DMF, 100 mM Tris, pH 7.4, 200 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.72 54.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.71 α = 90 b = 86.203 β = 90 c = 46.168 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 CCD MARMOSAIC 300 mm CCD 2015-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97853 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.6 27 100 0.095 38.3 14.3 30670 15.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 100 0.667 3.5 13.2
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 THROUGHOUT PDB entry 3NU3 1.613 24.772 1.36 30626 1508 99.07 0.1747 0.1735 0.1736 0.1967 0.1965 18.578
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 8.864 f_angle_d 1.039 f_chiral_restr 0.069 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction SCALEPACK data scaling