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Crystal structure of SARS-Cov-2 main protease in complex with PF00835231
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M HEPES 7.5, 20% PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.3 46.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.167 α = 90 b = 98.878 β = 107.996 c = 58.807 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2022-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 2.2 52.47 94.4 0.113 8.7 4.3 28537 35.3243323255
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 2.21 2.33 0.623
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.21 46.01 1.3567577388 28461 1378 94.2386013708 0.206838900954 0.204421265599 0.2075 0.254167326602 0.2565 40.8965424702
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 9.29189454141 f_angle_d 0.97335337683 f_chiral_restr 0.0539813013128 f_bond_d 0.00740796499747 f_plane_restr 0.00568482241772
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4470 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing