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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
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 3.36 63.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.226 α = 90 b = 81.836 β = 104.17 c = 53.425 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 2006-05-05 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 2.1 64.55 91.2 0.07 0.07 9.7 26214 23907
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 93.8 0.328 0.328 5.1 3821
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 2A5A 2.1 18.43 22259 1225 88.77 0.20066 0.19812 0.2215 0.24813 0.271 RANDOM 31.552
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] -4.12 0.51 5.44 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.216 r_dihedral_angle_4_deg 19.95 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_1_deg 6.89 r_scangle_it 2.364 r_scbond_it 1.652 r_angle_refined_deg 1.481 r_mcangle_it 1.084 r_mcbond_it 0.661 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.216 r_dihedral_angle_4_deg 19.95 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_1_deg 6.89 r_scangle_it 2.364 r_scbond_it 1.652 r_angle_refined_deg 1.481 r_mcangle_it 1.084 r_mcbond_it 0.661 r_nbtor_refined 0.305 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.198 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2417 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection MOSFLM data reduction SCALA data scaling MOLREP phasing