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SARS-CoV-2 3CL protease (3CLpro) in complex with Robinetin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M2N 6M2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM MES, pH5.5-6.5, 10%-25% PEG6000, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2 38.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.156 α = 90 b = 54.182 β = 100.89 c = 115.416 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 PILATUS 6M 2022-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
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 2.28 39.16 99.6 0.067 0.074 0.03 0.998 14.8 6.1 24439
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.41 99.5 0.233 0.254 0.101 0.986 6.2
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 FREE R-VALUE 6M2N 2.28 37.78 1.34 24333 1135 99.05 0.2461 0.2457 0.2469 0.2553 0.26
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 12.038 f_angle_d 0.638 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4449 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data reduction SCALA data scaling