7QF1

Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.6264


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6M0J6M0J, 5VAG
experimental modelPDB 5VAG6M0J, 5VAG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2960.1 M NaAc, 7% PEG 6000, 30% ethanol
Crystal Properties
Matthews coefficientSolvent content
4.9475.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.163α = 90
b = 191.319β = 90
c = 220.928γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 9M2020-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.9801SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.849.211000.4450.4530.0860.99610.427.471215
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.861006.776.8941.2980.42428

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 REPLACEMENTTHROUGHOUT6M0J, 5VAG2.848.211.3371035359199.850.22990.22860.25491.6965
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9632
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms39

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing