7M7W

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	30% Precipitant Mix 2 (Molecular Dimensions; ethylene glycol, PEG8000), 0.1 M Buffer System 3, pH 8.5 (Molecular Dimensions; Tris (base)/BICINE), 0.12 M Monosaccharides Mix (Molecular Dimensions), 0.02 M sodium chloride, 0.01 M MES, pH 6, 3% v/v Jeffamine ED-2003

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.185	α = 90
b = 66.402	β = 94.34
c = 237.659	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2021-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.65	63.94	98.6	0.149	0.161	0.06	0.997	10.9	6.9		77307

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)	Redundancy	Number Unique Reflections (All)
1	2.65	2.7	98.3		2.494	2.696	1.013	0.36		6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 7JX3, homology models of S2X259 Fab and S2H97 Fab	2.65	50.01	73189	3771	97.95	0.2236	0.2212	0.271	RANDOM	75.747

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]
1.49		1.2	-1.74		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.664
r_dihedral_angle_3_deg	15.912
r_dihedral_angle_4_deg	14.671
r_dihedral_angle_1_deg	6.69
r_angle_refined_deg	0.817
r_chiral_restr	0.065
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16162
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.