7JMW

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with cross-neutralizing antibody COVA1-16 Fab


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XC46XC4,4IMK,2Q20
experimental modelPDB 4IMK6XC4,4IMK,2Q20
experimental modelPDB 2Q206XC4,4IMK,2Q20

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.9293.1520% PEG 3350, 0.2 M Na-iodide, pH 6.9
Crystal Properties
Matthews coefficientSolvent content
2.7254.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.403α = 90
b = 124.905β = 96.101
c = 57.614γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-10.9795SSRLBL12-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.895097.90.1530.090.9637.43.71765642.71
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.892.950.6910.4290.6681.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6XC4,4IMK,2Q202.8942.771.351763294897.430.24070.23790.290847.36
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d8.3598
f_angle_d0.6772
f_chiral_restr0.0463
f_plane_restr0.0046
f_bond_d0.0032
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4845
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing