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Crystal structure of the main protease (3CLpro/Mpro) of SARS-CoV-2 obtained in presence of 5 mM X77, from an "old" crystal.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Sodium formate, 0.1M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate, 0.1M Potassium sodium tartrate tetrahydrate, 0.1M Sodium oxamate, 0.1 M Hepes/MOPS pH 7.5, 20% v/v Ethylene glycol, 10 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.848 α = 90 b = 101.138 β = 90 c = 104.258 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 PIXEL DECTRIS PILATUS 6M 2021-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.9999 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 101.14 100 0.083 0.999 14.8 9.1 79582 24.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 0.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 50.57 1.34 79486 4021 99.95 0.1712 0.1701 0.17 0.1914 0.1914 35.99
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 13.5901 f_angle_d 0.9314 f_chiral_restr 0.061 f_bond_d 0.0091 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4726 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing