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Crystal structure of MERS-CoV 3CL protease in spacegroup P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 298 0.2M Sodium formate, 0.1M BICINE pH8.5 20% PEG5000
Crystal Properties Matthews coefficient Solvent content 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.908 α = 90 b = 94.68 β = 90 c = 97.674 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 315r 2020-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979183 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.33814917992 61.85 100 0.055 13.7 8 32039 39.0028021821
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.46 0.439
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 4WMD 2.33814917992 61.8475803473 1.34350684801 31946 1616 99.8125351497 0.21629118908 0.213600281697 0.2152 0.266992896492 0.2697 43.0711832251
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.64635525645 f_angle_d 0.952941703179 f_chiral_restr 0.0546180824823 f_bond_d 0.00797257150615 f_plane_restr 0.00586332710612
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4476 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DENZO data reduction HKL-2000 data scaling PHENIX phasing