8BSF

CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7LDJ 
experimental modelPDB 5IBT 
experimental modelPDB 3ZL4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.04 M potassium dihydrogen phosphate 18 % PEG 8000 20 % glycerol
Crystal Properties
Matthews coefficientSolvent content
3.0759.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.693α = 90
b = 71.197β = 90.04
c = 121.245γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.9762MAX IVBioMAX

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.248.0798.90.0960.1040.0390.998137.144882
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)RedundancyNumber Unique Reflections (All)
12.22.2798.31.5681.690.6270.5757.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.248.0742690218998.690.197570.195880.22943RANDOM53.945
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]
1.440.260.16-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.049
r_dihedral_angle_4_deg19.888
r_dihedral_angle_3_deg15.941
r_long_range_B_other9.365
r_long_range_B_refined9.362
r_dihedral_angle_1_deg8.147
r_scangle_other7.385
r_mcangle_other6.713
r_mcangle_it6.711
r_scbond_it5.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.049
r_dihedral_angle_4_deg19.888
r_dihedral_angle_3_deg15.941
r_long_range_B_other9.365
r_long_range_B_refined9.362
r_dihedral_angle_1_deg8.147
r_scangle_other7.385
r_mcangle_other6.713
r_mcangle_it6.711
r_scbond_it5.096
r_scbond_other5.096
r_mcbond_it4.715
r_mcbond_other4.709
r_angle_refined_deg1.614
r_angle_other_deg1.241
r_chiral_restr0.064
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4606
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing