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A Mechanistic view of Enzyme Inhibition and Peptide Hydrolysis in the Active Site of the SARS-CoV 3C-Like peptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A5A PDB ENTRY 2A5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 50mM ammonium acetate, 5% polyethylene glycol (Mr10, 000), 3% ethylene glycol, 3% dimethyl sulfoxide, 1mM dithiothreitol, 0.1mM Mes (pH6.5), VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 3.34 63.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.565 α = 90 b = 81.459 β = 104.45 c = 53.359 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315 crystal 2006-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 0.97946 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.79 18.37 98.8 0.078 0.078 11.6 42339 41831
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 1.79 1.89 97.6 0.643 2.7 6186
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2A5A 1.79 18.37 39711 2111 98.7 0.19285 0.19049 0.2301 0.2387 0.2741 RANDOM 31.492
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] -2.23 0.91 3.13 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.162 r_dihedral_angle_4_deg 20.153 r_dihedral_angle_3_deg 15.453 r_dihedral_angle_1_deg 6.696 r_scangle_it 3.169 r_scbond_it 2.176 r_angle_refined_deg 1.7 r_mcangle_it 1.44 r_mcbond_it 0.924 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.162 r_dihedral_angle_4_deg 20.153 r_dihedral_angle_3_deg 15.453 r_dihedral_angle_1_deg 6.696 r_scangle_it 3.169 r_scbond_it 2.176 r_angle_refined_deg 1.7 r_mcangle_it 1.44 r_mcbond_it 0.924 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2427 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing