3SCK

Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION8.529520 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Crystal Properties
Matthew coefficientSolvent content
3.0159.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.219α = 90
b = 119.277β = 92.19
c = 113.236γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
135091.7467504287022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.1159.9

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 REPLACEMENTTHROUGHOUT347.2731946172378.710.241570.23920.28529RANDOM105.24
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]
3.69.6-2.32-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.17
r_dihedral_angle_4_deg18.292
r_dihedral_angle_3_deg16.585
r_dihedral_angle_1_deg2.863
r_scangle_it2.323
r_mcangle_it2.145
r_scbond_it1.392
r_angle_refined_deg1.329
r_rigid_bond_restr1.282
r_mcbond_it1.161
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.17
r_dihedral_angle_4_deg18.292
r_dihedral_angle_3_deg16.585
r_dihedral_angle_1_deg2.863
r_scangle_it2.323
r_mcangle_it2.145
r_scbond_it1.392
r_angle_refined_deg1.329
r_rigid_bond_restr1.282
r_mcbond_it1.161
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12514
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing