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Crystal structure of the SARS-CoV-2 main protease in complex with covalent tripeptidyl inhibitor NIP-22c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ALH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 19% PEG 4000, 0.1 M MES pH 6.5, 0.3 M dimethylethylammoniumpropane sulfonate (NDSB-195)
Crystal Properties Matthews coefficient Solvent content 2.08 40.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.88 α = 90 b = 53.96 β = 102.22 c = 47.51 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 2M 2022-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 1.12705 APS 21-ID-F
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 2.43 32.04 97.99 0.064 0.998 11.57 3.8 10360 57.07
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 2.43 2.47 0.668
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 2.43 32.04 1.38 10360 532 97.98 0.2058 0.2018 0.201 0.2775 0.2765 62.32
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 7.5232 f_angle_d 1.2767 f_chiral_restr 0.0537 f_bond_d 0.0132 f_plane_restr 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement xia2 data reduction pointless data scaling PHASER phasing REFMAC refinement