7KZB

Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1antibodies


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6W41 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293200 mM NaCl, 100 mM Tris (pH 8.0), 20% (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.4450

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.183α = 90
b = 147.674β = 90
c = 157.199γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.8349.3899.70.1440.150.0410.99812.413.528690
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.832.9898.21.2931.3420.3570.87313.8

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 REPLACEMENTTHROUGHOUT6w412.8349.3827165146299.620.25580.25140.3356RANDOM80.735
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]
1.06-0.53-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.267
r_dihedral_angle_3_deg20.345
r_dihedral_angle_4_deg19.396
r_dihedral_angle_1_deg8.196
r_angle_refined_deg1.733
r_angle_other_deg1.313
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.267
r_dihedral_angle_3_deg20.345
r_dihedral_angle_4_deg19.396
r_dihedral_angle_1_deg8.196
r_angle_refined_deg1.733
r_angle_other_deg1.313
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7101
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction