7FBK

Crystal structure of SARS-CoV-2 receptor binding domain N501Y mutant in complex with neutralizing nanobody 20G6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7FBJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.529370mM Citric acid, 30mM Bis-Tris propane pH 3.4, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4649.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.51α = 90
b = 90.531β = 90
c = 162.463γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97915SSRFBL18U1

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
11.919.8299.90.0730.0760.0210.99916.512.563067
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)
11.91.9499.70.9831.0460.3510.8498.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT7FBJ1.919.8259970303099.80.19890.19690.2394RANDOM50.554
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]
1.31-4.863.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.997
r_dihedral_angle_4_deg18.518
r_dihedral_angle_3_deg16.321
r_dihedral_angle_1_deg7.987
r_angle_refined_deg1.906
r_angle_other_deg1.389
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.997
r_dihedral_angle_4_deg18.518
r_dihedral_angle_3_deg16.321
r_dihedral_angle_1_deg7.987
r_angle_refined_deg1.906
r_angle_other_deg1.389
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4866
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing