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Mpro from SARS-CoV-2 with 4A 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, HANGING DROP 293 20% Polyethylene glycol monomethyl ether 5.000, 200 mM Potassium formate
Crystal Properties Matthews coefficient Solvent content 2.02 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.67 α = 90 b = 53.32 β = 101.97 c = 45.2 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 PILATUS3 6M 2022-10-06 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) 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 48.125 98.6 0.967 8.87 6.3 18323
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 2.08 0.346
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 1.981 48.125 18322 917 98.643 0.201 0.1974 0.1973 0.2663 0.2666 52.564
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] 2.504 0.483 -0.793 -1.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.522 r_dihedral_angle_3_deg 14.413 r_dihedral_angle_2_deg 11.688 r_lrange_it 9.461 r_lrange_other 9.461 r_dihedral_angle_1_deg 8.247 r_scangle_it 7.655 r_scangle_other 7.653 r_mcangle_it 6.226 r_mcangle_other 6.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.522 r_dihedral_angle_3_deg 14.413 r_dihedral_angle_2_deg 11.688 r_lrange_it 9.461 r_lrange_other 9.461 r_dihedral_angle_1_deg 8.247 r_scangle_it 7.655 r_scangle_other 7.653 r_mcangle_it 6.226 r_mcangle_other 6.224 r_scbond_it 5.417 r_scbond_other 5.416 r_mcbond_it 4.636 r_mcbond_other 4.636 r_angle_refined_deg 1.831 r_angle_other_deg 0.706 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.172 r_symmetry_nbd_other 0.16 r_nbd_other 0.116 r_symmetry_nbd_refined 0.105 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_refined 0.06 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2294 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing