3D0G

Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human 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
2.957.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.008α = 90
b = 119.762β = 96.22
c = 108.801γ = 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
12.85050660

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.847.1444939226293.810.2170.2140.279RANDOM74.503
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]
0.443.721.93-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.657
r_dihedral_angle_3_deg20.043
r_dihedral_angle_4_deg17.461
r_dihedral_angle_1_deg5.765
r_sphericity_free5.227
r_mcangle_it1.853
r_scangle_it1.8
r_angle_refined_deg1.27
r_scbond_it1.126
r_rigid_bond_restr1.055
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.657
r_dihedral_angle_3_deg20.043
r_dihedral_angle_4_deg17.461
r_dihedral_angle_1_deg5.765
r_sphericity_free5.227
r_mcangle_it1.853
r_scangle_it1.8
r_angle_refined_deg1.27
r_scbond_it1.126
r_rigid_bond_restr1.055
r_mcbond_it1.031
r_sphericity_bonded0.842
r_nbtor_refined0.315
r_nbd_refined0.229
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.145
r_chiral_restr0.09
r_metal_ion_refined0.059
r_symmetry_hbond_refined0.057
r_bond_refined_d0.01
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
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing