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Mpro from SARS-CoV-2 with 298Q 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 20% PEG 3350, 0.1 mM benzamidine hydrochloride, 200 mM potassium formate
Crystal Properties Matthews coefficient Solvent content 1.99 38.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.26 α = 90 b = 53.1 β = 102.54 c = 44.63 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 2022-10-06 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 1.52 47.95 90 0.99 11.7 2.45 36271
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 1.52 1.61 0.343 0.55
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 1.8 47.944 21969 1099 90.259 0.152 0.1482 0.1704 0.2276 0.2393 20.731
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] 0.356 -2.196 2.736 -1.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.075 r_dihedral_angle_6_deg 15.366 r_dihedral_angle_2_deg 14.097 r_dihedral_angle_1_deg 7.968 r_rigid_bond_restr 6.062 r_lrange_it 4.344 r_lrange_other 4.28 r_scangle_it 3.509 r_scangle_other 3.283 r_mcangle_it 2.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.075 r_dihedral_angle_6_deg 15.366 r_dihedral_angle_2_deg 14.097 r_dihedral_angle_1_deg 7.968 r_rigid_bond_restr 6.062 r_lrange_it 4.344 r_lrange_other 4.28 r_scangle_it 3.509 r_scangle_other 3.283 r_mcangle_it 2.945 r_mcangle_other 2.944 r_scbond_it 2.722 r_scbond_other 2.552 r_mcbond_it 2.194 r_mcbond_other 2.194 r_angle_refined_deg 2.107 r_angle_other_deg 0.999 r_nbd_refined 0.204 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.166 r_symmetry_nbd_other 0.154 r_nbd_other 0.128 r_symmetry_xyhbond_nbd_refined 0.119 r_chiral_restr 0.111 r_symmetry_nbd_refined 0.105 r_symmetry_nbtor_other 0.072 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2321 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing