7FCP

Crystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XDG6XDG, 7JMW
experimental modelPDB 7JMW6XDG, 7JMW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72910.05 M HEPES pH 7.0 20%(w/v) PEG3350 1%(w/v) Tryptone
Crystal Properties
Matthews coefficientSolvent content
2.5952.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.007α = 90
b = 80.414β = 106.23
c = 72.746γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-01-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNFPSS BEAMLINE BL19U10.97852NFPSSBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.4107.061000.080.0880.98122.46.348529
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4499.70.7190.7950.7512.25.4

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 REPLACEMENTTHROUGHOUT6XDG, 7JMW2.45044351224395.810.19350.1910.2446RANDOM40.402
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]
0.530.26-0.710.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.442
r_dihedral_angle_4_deg16.409
r_dihedral_angle_3_deg15.186
r_dihedral_angle_1_deg6.424
r_angle_other_deg3.853
r_angle_refined_deg1.389
r_chiral_restr0.258
r_gen_planes_other0.025
r_gen_planes_refined0.012
r_bond_refined_d0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.442
r_dihedral_angle_4_deg16.409
r_dihedral_angle_3_deg15.186
r_dihedral_angle_1_deg6.424
r_angle_other_deg3.853
r_angle_refined_deg1.389
r_chiral_restr0.258
r_gen_planes_other0.025
r_gen_planes_refined0.012
r_bond_refined_d0.009
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8170
Nucleic Acid Atoms
Solvent Atoms589
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction