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Crystal structure of CV3-25 Fab bound to SARS-CoV-2 spike stem helix peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MVZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Na Acetate:HCl, pH 4.5, 2.0M (NH4)2SO4, 0.01M SrCl
Crystal Properties Matthews coefficient Solvent content 2.96 58.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.173 α = 90 b = 60.173 β = 90 c = 285.825 γ = 120
Symmetry Space Group P 32 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 PILATUS 6M 2021-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0092 ALS 5.0.2
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 1.74 49.01 100 0.025 0.035 0.025 0.999 21.7 1.9 63310
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 1.74 1.77 100 0.309 0.437 0.309 0.67 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5MVZ 1.74 49.01 60094 3105 99.98 0.182 0.1809 0.1883 0.2028 0.2093 RANDOM 36.109
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] 0.05 0.02 0.05 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.669 r_dihedral_angle_4_deg 17.81 r_dihedral_angle_3_deg 13.273 r_dihedral_angle_1_deg 6.846 r_angle_refined_deg 1.764 r_angle_other_deg 1.043 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.669 r_dihedral_angle_4_deg 17.81 r_dihedral_angle_3_deg 13.273 r_dihedral_angle_1_deg 6.846 r_angle_refined_deg 1.764 r_angle_other_deg 1.043 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3471 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing