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Mpro from SARS-CoV-2 with 4Q mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG 3350, 200 mM magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.03 39.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.979 α = 90 b = 53.68 β = 100.819 c = 113.957 γ = 90
Symmetry Space Group I 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 PILATUS3 S 6M 2022-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.11 48.402 99.1 0.137 0.162 0.086 0.996 7.6 6.7 15279
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 2.11 2.17 2.153 2.538 1.328 0.439 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.113 48.402 15277 774 98.893 0.214 0.2102 0.2103 0.2806 0.2807 62.476
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] -3.47 1.387 -2.225 4.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.315 r_lrange_it 14.194 r_lrange_other 14.192 r_dihedral_angle_6_deg 13.726 r_dihedral_angle_2_deg 11.568 r_scangle_it 8.957 r_scangle_other 8.955 r_dihedral_angle_1_deg 8.298 r_mcangle_it 7.339 r_mcangle_other 7.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.315 r_lrange_it 14.194 r_lrange_other 14.192 r_dihedral_angle_6_deg 13.726 r_dihedral_angle_2_deg 11.568 r_scangle_it 8.957 r_scangle_other 8.955 r_dihedral_angle_1_deg 8.298 r_mcangle_it 7.339 r_mcangle_other 7.337 r_scbond_it 5.993 r_scbond_other 5.99 r_mcbond_it 5.238 r_mcbond_other 5.226 r_angle_refined_deg 1.652 r_angle_other_deg 0.685 r_nbd_refined 0.186 r_nbtor_refined 0.161 r_symmetry_nbd_other 0.152 r_xyhbond_nbd_refined 0.137 r_nbd_other 0.113 r_symmetry_xyhbond_nbd_refined 0.111 r_symmetry_nbd_refined 0.11 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.069 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2323 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing Aimless data scaling