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Apo-crystal structure of a wild-type South African HIV-1 subtype C protease at 2.4 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 5 mg/mL of wild-type South African HIV-1 subtype C protease in 10 mM of sodium acetate at pH 5 with the crystallization condition consisting of 0.1 M of bis-Tris at pH 6.5 and 3.0 M of NaCl
Crystal Properties Matthews coefficient Solvent content 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.6 α = 90 b = 46.6 β = 90 c = 102.144 γ = 90
Symmetry Space Group P 41 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 Bruker PHOTON III 2022-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS 3.0 MICROFOCUS 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.4 22.39 97.2 0.138 0.175 0.106 0.991 9.7 4.5 4659 36.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.462
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.4 22.39 1.33 4649 241 96.41 0.2059 0.2033 0.2079 0.221 0.2215 34.02
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 2.5913 f_angle_d 0.563 f_chiral_restr 0.0486 f_plane_restr 0.0035 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 755 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement SAINT data reduction SADABS data scaling PHASER phasing