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SARS-CoV-2 RBD in complex with a Fab fragment of a neutralising antibody mRBD2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BGF 3BGF, 6YM0 experimental model PDB 6YM0 3BGF, 6YM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 281 0.1 M Bis Tris Propane pH 6.5 0.2 M Potassium thiocyanate 20 % w/v PEG 3350 10 % v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.47 α = 90 b = 194.62 β = 97.16 c = 62.09 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2022-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 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 1.98 52.05 100 0.109 0.112 0.027 0.999 13.2 17.5 95377 59.19
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 1.98 2.03 100 9.628 9.922 2.378 0.329 17.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BGF, 6YM0 1.98 39.02 93639 4526 98.2 0.2492 0.2475 0.2385 0.284 0.2376 RANDOM 64.95
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] 2.0873 4.3613 -10.6259 8.5387
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.9 t_omega_torsion 3.58 t_angle_deg 0.99 t_bond_d 0.011 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9495 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 85
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing