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Crystal structure of unbound SARS coronavirus main peptidase in the space group C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UK2 PDB ENTRY 1UK2
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 3.36 63.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.758 α = 90 b = 82.14 β = 104.87 c = 53.128 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 1.115879 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 2.08 50 95.8 26196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.08 2.15 91
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 1UK2 2.08 40 24536 1296 95.86 0.19455 0.19171 0.2716 0.24638 0.3069 RANDOM 56.637
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] -3.77 2.62 5.1 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_3_deg 20.011 r_dihedral_angle_4_deg 17.573 r_dihedral_angle_1_deg 8.681 r_scangle_it 3.227 r_mcangle_it 3.181 r_angle_refined_deg 2.801 r_scbond_it 2.38 r_mcbond_it 2.25 r_symmetry_hbond_refined 0.371
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_3_deg 20.011 r_dihedral_angle_4_deg 17.573 r_dihedral_angle_1_deg 8.681 r_scangle_it 3.227 r_mcangle_it 3.181 r_angle_refined_deg 2.801 r_scbond_it 2.38 r_mcbond_it 2.25 r_symmetry_hbond_refined 0.371 r_nbtor_refined 0.349 r_nbd_refined 0.28 r_xyhbond_nbd_refined 0.262 r_symmetry_vdw_refined 0.235 r_chiral_restr 0.198 r_bond_refined_d 0.029 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2431 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing