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SARS-CoV-2 S stem helix peptide bound to Fab22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7M53 PDB entry 7M53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium citrate, pH 5.5, 23% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.57 52.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.246 α = 90 b = 73.08 β = 100.5 c = 89.043 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 80 CCD ADSC QUANTUM 315r 2021-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 87.55 97.3 0.987 5.1 3.6 38944 25.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.878
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 PDB entry 7M53 1.9 43.78 1.4 38918 1937 97.32 0.2062 0.2048 0.2048 0.2349 0.2343 38.5
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 16.188 f_angle_d 0.9517 f_chiral_restr 0.0592 f_plane_restr 0.0072 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3379 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement Coot model building iMOSFLM data reduction Aimless data scaling PHASER phasing