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Crystal structure of 084-7D Fab bound to SARS-CoV-2 Beta RBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 8.25% PEG 3350
4.95% MPD
0.2 M Lithium sulfate
0.1 M imidazole/hydrochloric acid pH 6.5
20% Ethylene glycol added after crystallization
Crystal Properties Matthews coefficient Solvent content 2.86 56.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.45 α = 90 b = 84.368 β = 90 c = 126.239 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 S 16M 2023-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 2.7 50 99.57 0.3974 0.4049 0.07671 0.995 8.47 27.3 24546 48.56
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 2.7 2.797 99 2.575 0.5071 0.611 26.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.7 50 1.34 24449 1223 99 0.2249 0.2226 0.2215 0.269 0.267 50.13
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 5.0461 f_angle_d 0.7484 f_chiral_restr 0.0495 f_bond_d 0.0059 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4638 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX model building PHENIX refinement xia2 data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction