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B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Potassium Chloride and 20% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.183 α = 90 b = 60.36 β = 93.63 c = 79.699 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 PIXEL DECTRIS PILATUS 300K 2020-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977410 ALS 5.0.1
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 1.27 46.5 93.1 0.033 0.039 0.021 1 10.1 3 107997 17.82
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 1.27 1.29 56.4 1.427 1.98 1.369 0.327 1.5
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 THROUGHOUT 6NB8 1.4 46.5 1.36 85652 4260 98.62 0.146 0.1443 0.1444 0.1739 0.175 28.0496
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 13.534 f_angle_d 1.361 f_chiral_restr 0.116 f_bond_d 0.014 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3370 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction