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)
Type	Source	Accession Code	Details
in silico model	Other		homology model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 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 coefficient	Solvent content
2.26	45.51

Crystal Data

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

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2020-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

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	1.38	48.15	99.3	0.059	0.064	0.024	0.999	19.1	13.1		89367

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	1.38	1.4	87.8		2.115	2.295	0.881	0.74	1.2

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	homology model	1.38	40	84581	4458	99.72	0.2002	0.1993	0.215	RANDOM	27.198

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]
-0.73			1.63		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.257
r_dihedral_angle_4_deg	18.295
r_dihedral_angle_3_deg	12.351
r_dihedral_angle_1_deg	7.375
r_angle_other_deg	1.237
r_angle_refined_deg	1.226
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.257
r_dihedral_angle_4_deg	18.295
r_dihedral_angle_3_deg	12.351
r_dihedral_angle_1_deg	7.375
r_angle_other_deg	1.237
r_angle_refined_deg	1.226
r_chiral_restr	0.046
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3339
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	14

Software

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

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 R01GM157729.