7PKI

Crystal structure of human ACE2 bound to the spike receptor-binding domain from a cave bat sarbecovirus closely related to SARS-CoV-2.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6M0J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5277.150.2 M Lithium sulfate, 0.1 M Tris 8.5, 30 % w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
6.1780

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 341.535α = 90
b = 341.535β = 90
c = 68.153γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 16M2021-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.978SOLEILPROXIMA 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
12.94249.6386.980.050.99611.4224364568.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.9423.0474.5620.496

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-VALUE6M0J2.9423413344449.29633104691.3435245511843635216987.01938417360.215016891360.2143703710420.22719605633364.6809885402
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_d14.3148713288
f_angle_d0.879974644649
f_chiral_restr0.0436209670625
f_bond_d0.00502197216593
f_plane_restr0.00454924285799
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6418
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms184

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
autoBUSTERphasing