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Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other M8b-A10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 297 2% v/v 1,4-dioxane
0.1M Tris pH 8.0
15% (w/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.159 α = 90 b = 127.194 β = 127.72 c = 75.431 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 DECTRIS EIGER2 XE 16M 2024-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 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 2.56 37.99 98.5 0.082 0.088 0.032 0.999 11.7 7.2 24650 70.34
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 2.59 2.71 94.5 0.983 1.059 0.39 0.775 7.1
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 2.59 37.99 1.35 24625 1999 98.33 0.2286 0.2259 0.2248 0.2572 0.2553 73.94
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 5.0398 f_angle_d 0.5428 f_chiral_restr 0.044 f_plane_restr 0.0039 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4914 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Blu-Ice data collection