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Dual Modes of Modification of Hepatitis A Virus 3C Protease by a Serine-Derived betaLactone: Selective Crystallization and High-resolution Structure of the His-102 Adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HAV PDB ENTRY 1HAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 297 PEG 8000, Tris-HCl, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.1 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.249 α = 90 b = 56.022 β = 90 c = 80.649 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 4 2000-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.8857 SSRL BL9-2
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 1.4 20 97.7 0.037 13.6 40672 39711 5 5
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) 1.4 1.44 98 0.211 5.8
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 (All) 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 1HAV 1.4 18.35 36721 36721 2601 98.81 0.18619 0.18619 0.16626 0.1895 0.18757 0.1736 RANDOM 16.381
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] 0.03 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.483 r_dihedral_angle_4_deg 15.521 r_dihedral_angle_3_deg 11.197 r_dihedral_angle_1_deg 5.807 r_scangle_it 1.951 r_scbond_it 1.19 r_angle_refined_deg 0.986 r_mcangle_it 0.972 r_rigid_bond_restr 0.747 r_sphericity_free 0.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.483 r_dihedral_angle_4_deg 15.521 r_dihedral_angle_3_deg 11.197 r_dihedral_angle_1_deg 5.807 r_scangle_it 1.951 r_scbond_it 1.19 r_angle_refined_deg 0.986 r_mcangle_it 0.972 r_rigid_bond_restr 0.747 r_sphericity_free 0.581 r_mcbond_it 0.567 r_sphericity_bonded 0.432 r_nbtor_refined 0.305 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.083 r_symmetry_hbond_refined 0.069 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1634 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing