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SARS-CoV-2 3CL Protease complexed with covalent inhibitor BC671
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100mM sodium potassium tartrate, 10% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.02 39.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.738 α = 90 b = 53.522 β = 102.22 c = 45.939 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 PIXEL DECTRIS PILATUS 6M 2021-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
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 2.36 34.48 98.8 0.049 8.5 3.3 11119 51.44
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 2.36 2.45 0.45 2.1
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 2.36 34.48 1.36 11097 1111 98.75 0.2006 0.1941 0.1944 0.2581 0.258 60.91
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 8.2457 f_angle_d 1.2723 f_chiral_restr 0.0591 f_plane_restr 0.0138 f_bond_d 0.0133
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2323 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing