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An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A4O PDB ENTRY 2A4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 297 2.5% PEG 8000, 1.5% Glycerol, 10mM tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.15 42.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.672 α = 90 b = 56.055 β = 90 c = 80.974 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 210 2004-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.35 26.49 81.2 0.056 12.7 36919
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 1.35 1.4 22.6 0.307 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2A4O 1.39 26.49 34342 34294 1838 86.7 0.182 0.181 0.1804 0.197 0.186 RANDOM 20.97
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] 1.22 -0.55 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.315 r_dihedral_angle_4_deg 20.304 r_dihedral_angle_3_deg 11.773 r_dihedral_angle_1_deg 6.008 r_scangle_it 5.829 r_scbond_it 3.98 r_mcangle_it 2.905 r_mcbond_it 1.899 r_angle_refined_deg 1.2 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.315 r_dihedral_angle_4_deg 20.304 r_dihedral_angle_3_deg 11.773 r_dihedral_angle_1_deg 6.008 r_scangle_it 5.829 r_scbond_it 3.98 r_mcangle_it 2.905 r_mcbond_it 1.899 r_angle_refined_deg 1.2 r_nbtor_refined 0.307 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.142 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1667 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing