7KFY

Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-F10 Fab)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5 mother liquor composition (equal volume): 0.10% (w/v) n-Octyl-B-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 4.5, 22% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.362.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.74α = 90
b = 146.801β = 90
c = 144.593γ = 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
12.157200940.1180.1570.9916.172.0648373-3
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)
12.1572.2989.40.370.711.96

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 REPLACEMENTTHROUGHOUT7KFV2.15774.0448373258597.90.20780.20540.2486RANDOM52.24
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]
-8.20576.0382.1677
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion16.81
t_omega_torsion3.74
t_angle_deg1
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 Atoms4836
Nucleic Acid Atoms
Solvent Atoms532
Heterogen Atoms14

Software

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