2AJF

Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100 mM Tris pH 8.2, 24% PEG6000, 150 mM NaCl, 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, pH 7.5, pH 7.50
Crystal Properties
Matthew coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.299α = 90
b = 119.429β = 91.97
c = 113.237γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002005-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.847.493.10.08520.56.941841
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.993.10.6821.83

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1R422.947.441841216592.40.2210.2180.275RANDOM90.77
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]
0.457.050.04-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.497
r_dihedral_angle_3_deg20.62
r_dihedral_angle_4_deg17.319
r_dihedral_angle_1_deg5.69
r_scangle_it1.433
r_angle_refined_deg1.253
r_mcangle_it1.234
r_scbond_it0.855
r_mcbond_it0.678
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.497
r_dihedral_angle_3_deg20.62
r_dihedral_angle_4_deg17.319
r_dihedral_angle_1_deg5.69
r_scangle_it1.433
r_angle_refined_deg1.253
r_mcangle_it1.234
r_scbond_it0.855
r_mcbond_it0.678
r_nbtor_refined0.317
r_symmetry_hbond_refined0.24
r_nbd_refined0.234
r_symmetry_vdw_refined0.22
r_xyhbond_nbd_refined0.17
r_metal_ion_refined0.167
r_chiral_restr0.089
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_metal_ion_other
r_nbd_other
r_symmetry_vdw_other
r_angle_other_deg
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbtor_other
r_mcbond_other
r_gen_planes_other
r_bond_other_d
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12546
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms166

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing