7KFX

Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 Fab)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.6293protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl pH 7.5 mother liquor composition (equal volume): 0.03 M Citric acid, 0.07M BIS-TRIS propane/pH 7.6, 20% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.1360.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.455α = 90
b = 149.192β = 90
c = 146.143γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 16M2020-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9792APS24-ID-C

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
12.2220099.10.1360.1590.9956.863.5844541-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.222.3697.10.2510.613.56

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 REPLACEMENTTHROUGHOUT7KFV2.22674.644541212198.90.19260.19090.2261RANDOM63.35
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]
-8.7707-4.807513.5782
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion16.82
t_omega_torsion3.56
t_angle_deg1.01
t_bond_d0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_sum_occupancies
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4861
Nucleic Acid Atoms
Solvent Atoms325
Heterogen Atoms14

Software

Software
Software NamePurpose
BUSTERrefinement
PHENIXdata processing
Omodel building
XDSdata reduction
XDSdata scaling
PHASERphasing