☰ Navigation Tabs
Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-44 and Beta-54 Fabs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Citric acid pH 3.5 and 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.19 61.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.377 α = 90 b = 112.567 β = 90 c = 99.854 γ = 90
Symmetry Space Group P 21 21 2
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 2021-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97627 Diamond I03
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 2.26 65 99.5 0.096 0.029 0.974 14.2 12.3 68653 65.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.3 0.265 0.3
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 7BEP 2.26 49.93 1.33 67047 3455 97.21 0.2166 0.2153 0.2152 0.2401 0.2418 79.59
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 11.8422 f_angle_d 0.5529 f_chiral_restr 0.0424 f_plane_restr 0.0044 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8028 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 59
Software Software Software Name Purpose GDA data collection PHENIX refinement GDA data collection xia2 data reduction xia2 data scaling PHASER phasing