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Crystal structure of SARS-Cov-2 main protease D48N mutant in complex with PF07321332
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M HEPES 7.5, 20% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.67 53.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.152 α = 90 b = 102.656 β = 90 c = 103.355 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 9M 2022-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.07 72.83 94.4 0.037 15.7 10.3 42254 31.4738586135
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.2 0.861
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 7DQZ 2.07 56.9175 1.34493102168 42172 3783 94.3345313144 0.212352500906 0.21094691164 0.2133 0.240304093051 0.2407 36.3047455827
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.98143205237 f_angle_d 0.93436544951 f_chiral_restr 0.0505219945251 f_bond_d 0.00760586657963 f_plane_restr 0.00631824660968
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4388 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing