3D0I

Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.5298100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.9458.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.424α = 90
b = 119.824β = 95.5
c = 109.772γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97924APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.95046550

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.936.4741328205289.920.2270.2240.278RANDOM84.359
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]
1.94.711.06-2.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.69
r_dihedral_angle_4_deg18.69
r_dihedral_angle_3_deg17.918
r_sphericity_free4.237
r_dihedral_angle_1_deg3.826
r_scangle_it2.379
r_mcangle_it2.277
r_scbond_it1.704
r_rigid_bond_restr1.454
r_mcbond_it1.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.69
r_dihedral_angle_4_deg18.69
r_dihedral_angle_3_deg17.918
r_sphericity_free4.237
r_dihedral_angle_1_deg3.826
r_scangle_it2.379
r_mcangle_it2.277
r_scbond_it1.704
r_rigid_bond_restr1.454
r_mcbond_it1.288
r_angle_refined_deg1.243
r_sphericity_bonded0.656
r_nbtor_refined0.324
r_symmetry_vdw_refined0.296
r_nbd_refined0.263
r_symmetry_hbond_refined0.253
r_xyhbond_nbd_refined0.156
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12518
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction