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Structure of the apo form of Mpro from SARS-CoV-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K3T 7K3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 0.1 M sodium HEPES at pH 7.0 containing 22% PEG 4000 and 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2 38.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.873 α = 90 b = 53.629 β = 100.827 c = 114.688 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 PILATUS 6M 2022-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97625 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.86 38.68 97.1 0.998 10.06 5.92 43744
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 1.86 1.98 92.5 0.595 1.08 5.64
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7K3T 1.863 38.68 42906 2105 95.254 0.195 0.1922 0.2012 0.2534 0.2554 38.503
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] 0.689 0.194 -0.532 -0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.16 r_dihedral_angle_3_deg 16.879 r_dihedral_angle_6_deg 15.761 r_lrange_it 8.757 r_lrange_other 8.754 r_dihedral_angle_1_deg 7.694 r_scangle_it 6.787 r_scangle_other 6.786 r_mcangle_other 4.848 r_mcangle_it 4.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.16 r_dihedral_angle_3_deg 16.879 r_dihedral_angle_6_deg 15.761 r_lrange_it 8.757 r_lrange_other 8.754 r_dihedral_angle_1_deg 7.694 r_scangle_it 6.787 r_scangle_other 6.786 r_mcangle_other 4.848 r_mcangle_it 4.847 r_scbond_it 4.734 r_scbond_other 4.731 r_mcbond_it 3.616 r_mcbond_other 3.612 r_angle_refined_deg 1.582 r_angle_other_deg 0.862 r_symmetry_xyhbond_nbd_other 0.414 r_nbd_other 0.231 r_symmetry_nbd_refined 0.229 r_nbd_refined 0.227 r_symmetry_nbd_other 0.226 r_xyhbond_nbd_refined 0.219 r_nbtor_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.17 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.073 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4736 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing