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Room-temperature structure of SARS-CoV-2 Main protease at 104 MPa helium gas pressure in a sapphire capillary
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl was equilibrated against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ratio of malonic acid, imidazole, and boric acid), pH 7.5, containing 25% v/v PEG 1500 and 5% v/v DMSO. To achieve reproducible crystal growth seeding was used. Crystals appeared within a few hours and reached their final size after 2 -3 days.
Crystal Properties Matthews coefficient Solvent content 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.58 α = 90 b = 54.5 β = 101.246 c = 45.05 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 295 PIXEL DECTRIS PILATUS3 X CdTe 2M 2021-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.477 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.35 25.95 97.6 0.2854 0.3003 0.08828 0.985 8.4 10.2 11116 41.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.434 86.87 1.823 1.963 0.6839 0.375 1.19 6.5
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 FREE R-VALUE 7AR5 2.35 25.95 1.35 11116 1111 97.71 0.1797 0.1753 0.1761 0.2188 0.2198 60.71
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 12.1126 f_angle_d 0.5589 f_chiral_restr 0.0402 f_plane_restr 0.0035 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 8
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing