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Crystal structure of FD20, a neutralizing single-chain variable fragment (scFv) in complex with SARS-CoV-2 Spike receptor-binding domain (RBD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MOJ 6MOJ, 5C6W experimental model PDB 5C6W 6MOJ, 5C6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M lithium sulfate monohydrate, 0.1 M Bis-Tris pH 5.5, 25% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.958 α = 90 b = 57.925 β = 100.433 c = 47.207 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 100 PIXEL PSI PILATUS 6M 2020-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.13 46.43 98.89 0.2724 0.1322 0.979 5.65 5.2 9847 65.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.13 3.24 94.68 1.125 0.5387 0.791 1.5 5.3
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 6MOJ, 5C6W 3.13 46.43 1.35 9764 461 98.92 0.2529 0.2518 0.2543 0.2762 0.2826 61.91
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 17.7798 f_angle_d 0.7944 f_chiral_restr 0.0525 f_plane_restr 0.0044 f_bond_d 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3166 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing