7K8Q

Crystal structure of an anti-SARS-CoV-2 human neutralizing antibody Fab fragment, C121


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5T3ZPDB entry 5T3Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.12980.2 M ammonium citrate, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.0659.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.304α = 90
b = 71.304β = 90
c = 404.844γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-11.0SSRLBL12-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1239.199.20.0580.1140.9958.426.34223347.81
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051.360.810.9770.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-VALUEPDB entry 5T3Z236.361.3342233205998.740.20720.20540.243153.47
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_d21.3759
f_angle_d0.9956
f_chiral_restr0.0616
f_bond_d0.008
f_plane_restr0.0056
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3247
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms6

Software

Software
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing