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Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment C098
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XC4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 2.0 M ammonium sulfate, citric acid pH 3.5
Crystal Properties Matthews coefficient Solvent content 2.54 51.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.1 α = 90 b = 88.1 β = 90 c = 216.246 γ = 120
Symmetry Space Group P 65 2 2
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 2021-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.98 SSRL BL12-2
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 1.42 76.3 99.6 0.079 0.081 0.02 0.999 17.4 16.5 93013
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 1.42 1.45 99.2 2.079 2.143 0.514 0.637 17
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 6XC4 1.42 44.05 1.34 92886 4566 99.4 0.1864 0.1855 0.1888 0.2052 0.2071 34.3795
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 20.264 f_angle_d 1.169 f_chiral_restr 0.09 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3243 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing