7K3Q

An ultra-potent human neutralizing antibody locks the SARS-CoV-2 spike in the closed conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelOtherhomology model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Magnesium chloride hexahydrate, 0.1 M TRIS pH 8.5, 30% (w/v) PEG 4000 Condition A1 of Molecular Dimensions SG1 HT-96 Eco Screen
Crystal Properties
Matthews coefficientSolvent content
2.2645.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.014α = 90
b = 85.722β = 90
c = 86.306γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.0SLSX10SA

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
11.3848.1599.30.0590.0640.0240.99919.113.189367
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)
11.381.487.82.1152.2950.8810.741.2

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 REPLACEMENTTHROUGHOUThomology model1.384084581445899.720.20020.19930.215RANDOM27.198
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]
-0.731.63-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.257
r_dihedral_angle_4_deg18.295
r_dihedral_angle_3_deg12.351
r_dihedral_angle_1_deg7.375
r_angle_other_deg1.237
r_angle_refined_deg1.226
r_chiral_restr0.046
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.257
r_dihedral_angle_4_deg18.295
r_dihedral_angle_3_deg12.351
r_dihedral_angle_1_deg7.375
r_angle_other_deg1.237
r_angle_refined_deg1.226
r_chiral_restr0.046
r_bond_refined_d0.004
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 Atoms3339
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction