7JMX

Crystal structure of a SARS-CoV-2 cross-neutralizing antibody COVA1-16 Fab


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IMK4IMK,2Q20
experimental modelPDB 2Q204IMK,2Q20

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6293.1520% glycerol, 20% PEG-4000, 0.16 M NH4-sulfate, 0.08 M acetate pH 4.6
Crystal Properties
Matthews coefficientSolvent content
3.2261.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.287α = 90
b = 156.287β = 90
c = 156.287γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-06-24MSINGLE 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
12.53501000.2360.0380.99621.5372235740.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.532.580.5430.521

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-VALUE4IMK,2Q202.5330.651.3521874106998.090.21310.21150.243943.02
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_d3.7629
f_angle_d1.0094
f_chiral_restr0.0573
f_bond_d0.0072
f_plane_restr0.0059
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3223
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms19

Software

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