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The HIV protease inhibitor lopinavir binding to the active site of Cryphonectria parasitica endothiapepsin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 24% (w/v) PEG 4000, 0.1 M ammonium acetate and 0.1 M sodium acetate pH 4.6 were mixed with an equal volume of 6 mg/ml endothiapepsin solution. Microseeding was applied. After 2 days crystals were soaked with the ligand in reservoir solution in the presence of 5% (v/v) DMSO.
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.539 α = 90 b = 73.519 β = 110.139 c = 53.41 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 16M 2024-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033190 PETRA III, DESY P11
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 1.5 42.75 97.4 0.047 0.998 20.77 3.4 101583 11.07
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 1.5 1.54 0.113 0.987
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 FREE R-VALUE 1.5 42.75 1.42 101579 1999 97.52 0.1499 0.1497 0.1507 0.1588 0.1613 13.49
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 8.2261 f_angle_d 0.8216 f_chiral_restr 0.0572 f_plane_restr 0.0057 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2389 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing