8J5J

The crystal structure of bat coronavirus RsYN04 RBD bound to the antibody S43


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KFV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.2 M Potassium nitrate, 20% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
3.4664.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.373α = 90
b = 68.373β = 90
c = 240.863γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.979183SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
136699.80.12320.313.92169943.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1331.819

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE327.551.3421635215599.220.22750.22720.230643.97
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.7675
f_angle_d0.7658
f_chiral_restr0.0487
f_plane_restr0.0075
f_bond_d0.0043
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2486
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms14

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing