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The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other RBD structure from the authors experimental model PDB 6H71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293 22,5 % PEG 8000, 100mM NaAc pH 4.5, 200mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.21 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.664 α = 90 b = 97.664 β = 90 c = 64.35 γ = 120
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 PILATUS3 6M 2023-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 1.21 48.832 97.22 0.044 0.046 0.015 0.9996 22.245 9.89 103166 14.87
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 1.21 1.231 100 0.814 0.868 0.3 0.8234 2.212 8.33
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 1.21 42.29 1.36 103164 5193 97.22 0.1534 0.1525 0.1535 0.1696 0.1699 23.71
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 6.9675 f_angle_d 1.2159 f_chiral_restr 0.1015 f_plane_restr 0.0129 f_bond_d 0.0115
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2439 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 26
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing