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SARS-CoV-2 Main Protease in complex with a cyclic peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 22% PEG 3350, 0.1M Bis-Tris pH 6.0, 0.3M NaCl
Crystal Properties Matthews coefficient Solvent content 2 38.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.36 α = 90 b = 201.726 β = 113.49 c = 60.543 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2021-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 33.62 99.9 0.254 0.275 0.103 0.989 6.4 7 44063
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 2.43 99.6 1.542 1.667 0.629 0.512 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7JKV 2.35 33.62 41708 2306 99.58 0.1738 0.1707 0.2308 0.2143 RANDOM 34.931
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] -18.66 -2.82 52.99 -34.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.064 r_dihedral_angle_3_deg 22.233 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_1_deg 8.957 r_angle_refined_deg 1.727 r_angle_other_deg 1.373 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.064 r_dihedral_angle_3_deg 22.233 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_1_deg 8.957 r_angle_refined_deg 1.727 r_angle_other_deg 1.373 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9729 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing