6XC2

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZD34ZD3, 6YLA
experimental modelPDB 6YLA4ZD3, 6YLA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298.150.1M sodium citrate pH 5.5 15% polyethylene glycol 6000
Crystal Properties
Matthews coefficientSolvent content
2.8456.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.699α = 90
b = 143.494β = 118.68
c = 81.469γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-05-30MSINGLE 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 Merge I (Observed)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
13.115088.30.160.977.41.525802
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)
13.23.270.62

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 REPLACEMENTTHROUGHOUT4ZD3, 6YLA3.11240.3431.3825777128988.320.21620.21340.267470
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 Atoms9558
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms28

Software

Software
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing