7SD5

Crystallographic structure of neutralizing antibody 10-40 in complex with SARS-CoV-2 spike receptor binding domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7L5BPDB entry 7L5B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.53100.2 M potassium thiocyanate, 0.1 M sodium acetate, pH 5.5, 8% PEG550 MME, 8% PEG20000
Crystal Properties
Matthews coefficientSolvent content
2.5852.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.756α = 90
b = 79.845β = 90
c = 118.864γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5359.4497.10.045117.57.411188925.84
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.530.256

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 7L5B1.5359.44106248552096.770.177730.176270.20625RANDOM29.157
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]
-0.50.060.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.779
r_dihedral_angle_4_deg20.777
r_dihedral_angle_3_deg11.765
r_dihedral_angle_1_deg7.416
r_long_range_B_refined7.061
r_long_range_B_other6.936
r_scangle_other5.532
r_scbond_it3.799
r_scbond_other3.798
r_mcangle_it3.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.779
r_dihedral_angle_4_deg20.777
r_dihedral_angle_3_deg11.765
r_dihedral_angle_1_deg7.416
r_long_range_B_refined7.061
r_long_range_B_other6.936
r_scangle_other5.532
r_scbond_it3.799
r_scbond_other3.798
r_mcangle_it3.414
r_mcangle_other3.414
r_mcbond_it2.515
r_mcbond_other2.515
r_angle_refined_deg1.783
r_angle_other_deg1.477
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4851
Nucleic Acid Atoms
Solvent Atoms678
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing