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X-ray structure of SARS-CoV-2 main protease covalently bound to compound GRL-051-22 at 1.75 A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9E7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 12% PEG 10K, 0.003 M DTT, 1% MPD, 0.05 M MES (pH 6.0), 0.12 M KCl, 2.5% DMSO, 25 mM HEPES, protein concentration 5.5 mg/mL
Crystal Properties Matthews coefficient Solvent content 2.87 57.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.772 α = 90 b = 82.168 β = 126.316 c = 54.415 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 EIGER2 S 4M confocal VariMax-VHF Arc)Sec optics 2024-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.75 27.3 88.73 0.0796 0.09579 0.05205 0.97 12.62 3.1 46796 24.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 99.62 0.9663 0.7869 0.576 0.72 2.1
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 1.75 27.3 1.35 34204 1708 88.73 0.1807 0.1786 0.1813 0.2187 0.2185 33.16
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 17.1817 f_angle_d 1.1278 f_chiral_restr 0.057 f_plane_restr 0.0117 f_bond_d 0.0109
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHENIX phasing