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Crystal structure of SARS-Cov-2 main protease M49I mutant in complex with GC376
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.12~0.21M PEG3350,20%~24%Na2SO4
Crystal Properties Matthews coefficient Solvent content 2.35 47.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.446 α = 90 b = 99.225 β = 108.454 c = 59.558 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 S 9M 2022-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 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 1.68 56.5 86.3 0.064 15.5 6.6 60444 24.4323277942
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 1.68 1.77 0.906
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 1.68 46.55 1.34366372386 60327 2969 86.0474404142 0.216662337138 0.215173786041 0.2154 0.24721963173 0.2446 30.5960112407
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 8.80387403654 f_angle_d 0.886921998315 f_chiral_restr 0.052897666574 f_plane_restr 0.00680665148065 f_bond_d 0.006433913095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4493 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing