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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 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.98 α = 90 b = 53.933 β = 101.004 c = 44.738 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 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 1.98 48.71 98.6 0.987 7.75 4.83 18561
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 1.98 2.1 93.7 0.385 0.73 4.66
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 1.99 48.71 18512 900 99.473 0.216 0.212 0.2205 0.2859 0.2847 49.743
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] 0.822 -1.131 0.917 -1.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.882 r_dihedral_angle_3_deg 16.425 r_dihedral_angle_6_deg 16.307 r_lrange_it 8.494 r_lrange_other 8.484 r_dihedral_angle_1_deg 8.019 r_scangle_it 5.894 r_scangle_other 5.892 r_mcangle_other 5.428 r_mcangle_it 5.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.882 r_dihedral_angle_3_deg 16.425 r_dihedral_angle_6_deg 16.307 r_lrange_it 8.494 r_lrange_other 8.484 r_dihedral_angle_1_deg 8.019 r_scangle_it 5.894 r_scangle_other 5.892 r_mcangle_other 5.428 r_mcangle_it 5.427 r_scbond_it 4.091 r_scbond_other 4.09 r_mcbond_it 4.005 r_mcbond_other 3.994 r_angle_refined_deg 1.324 r_angle_other_deg 0.733 r_nbd_other 0.235 r_symmetry_nbd_other 0.217 r_nbd_refined 0.211 r_symmetry_nbd_refined 0.2 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.059 r_symmetry_xyhbond_nbd_other 0.021 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2358 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing