8DWA

Crystal structure of neutralizing antibody P1D9 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7SD5PDB entry 7SD5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 18% w/v PEG5000 MME
Crystal Properties
Matthews coefficientSolvent content
2.9558.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.136α = 90
b = 147.136β = 90
c = 80.108γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2022-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.979180APS24-ID-C

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
13.12144.151000.5160.5270.1040.9916.925.615333
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)
13.123.341004.524.6070.8870.43726.7

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 7SD53.263.551418774799.390.237880.234780.29747RANDOM94.464
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]
1.241.24-2.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.803
r_dihedral_angle_3_deg19.287
r_dihedral_angle_4_deg16.276
r_long_range_B_refined10.726
r_long_range_B_other10.726
r_dihedral_angle_1_deg8.465
r_scangle_other4.923
r_mcangle_it4.436
r_mcangle_other4.435
r_scbond_it2.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.803
r_dihedral_angle_3_deg19.287
r_dihedral_angle_4_deg16.276
r_long_range_B_refined10.726
r_long_range_B_other10.726
r_dihedral_angle_1_deg8.465
r_scangle_other4.923
r_mcangle_it4.436
r_mcangle_other4.435
r_scbond_it2.896
r_scbond_other2.896
r_mcbond_other2.622
r_mcbond_it2.621
r_angle_refined_deg1.539
r_angle_other_deg1.187
r_chiral_restr0.236
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4584
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction