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Crystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide in the space group C2
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 6.5 298 ammonium acetate, PEG 10000, ethylene glycol, dimethyl sulfoxide, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.35 63.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.703 α = 90 b = 83.677 β = 105.65 c = 52.862 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 210 2004-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115869 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.88 50 96.3 35576
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.95 90
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 1.88 40 32587 1710 94.21 0.20034 0.19813 0.2638 0.24224 0.289 RANDOM 43.973
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] -2.42 1.19 3.69 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.259 r_dihedral_angle_4_deg 17.907 r_dihedral_angle_3_deg 16.83 r_dihedral_angle_1_deg 6.615 r_mcangle_it 2.681 r_scangle_it 2.624 r_angle_refined_deg 2.342 r_scbond_it 2.002 r_mcbond_it 1.919 r_nbtor_refined 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.259 r_dihedral_angle_4_deg 17.907 r_dihedral_angle_3_deg 16.83 r_dihedral_angle_1_deg 6.615 r_mcangle_it 2.681 r_scangle_it 2.624 r_angle_refined_deg 2.342 r_scbond_it 2.002 r_mcbond_it 1.919 r_nbtor_refined 0.34 r_symmetry_hbond_refined 0.329 r_symmetry_vdw_refined 0.308 r_nbd_refined 0.3 r_xyhbond_nbd_refined 0.261 r_chiral_restr 0.192 r_bond_refined_d 0.022 r_gen_planes_refined 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing