3D0H

Crystal structure of spike protein receptor-binding domain from the 2002-2003 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
2.9357.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.352α = 90
b = 119.841β = 95.89
c = 109.42γ = 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
13.137.538826

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 DIFFRACTIONTHROUGHOUT3.137.533878172690.310.2250.2210.302RANDOM75.25
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]
1.294.350.99-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.386
r_dihedral_angle_4_deg20.556
r_dihedral_angle_3_deg18.757
r_dihedral_angle_1_deg4.844
r_sphericity_free4.538
r_scangle_it2.173
r_mcangle_it2.113
r_scbond_it1.444
r_angle_refined_deg1.293
r_rigid_bond_restr1.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.386
r_dihedral_angle_4_deg20.556
r_dihedral_angle_3_deg18.757
r_dihedral_angle_1_deg4.844
r_sphericity_free4.538
r_scangle_it2.173
r_mcangle_it2.113
r_scbond_it1.444
r_angle_refined_deg1.293
r_rigid_bond_restr1.258
r_mcbond_it1.187
r_sphericity_bonded0.686
r_symmetry_hbond_refined0.358
r_nbtor_refined0.322
r_symmetry_vdw_refined0.27
r_nbd_refined0.259
r_xyhbond_nbd_refined0.15
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12522
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction