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. 2021 Mar 12;29(5):819–833.e7. doi: 10.1016/j.chom.2021.03.005
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

1-68 Liu et al., 2020a N/A
1-87 Liu et al., 2020a N/A
2-17 Liu et al., 2020a N/A
2-51 Liu et al., 2020a N/A
4-8 Liu et al., 2020a N/A
4-18 Liu et al., 2020a N/A
5-24 Liu et al., 2020a N/A
4A8 Chi et al., 2020 N/A

Bacterial and virus strains

VSV-G pseudo-typed ΔG-luciferase Kerafast Cat# EH1020-PM

Chemicals, peptides, and recombinant proteins

SARS-CoV-2 spike protein Wrapp et al., 2020b N/A
Polyethylenimine Polysciences Cat# 24765-2
Freestyle 293 Expression Media Thermo Scientific Cat# 12338-026
Expi293 Expression Medium Thermo Scientific Cat# A14635
Dulbecco’s Modified Eagle Medium ATCC Cat# 30-2002
Fetal Bovine Serum, heat inactivated Thermo Scientific Cat# 16140071
Opti-MEM™ Reduced Serum Media Thermo Scientific Cat# 31985-070
IMAC Sepharose 6 Fast Flow GE Healthcare Cat# 17092109
Tris Base Thermo Scientific Cat# BP152-5
Sodium Chloride Thermo Scientific Cat# S271-10
Imidazole ACROS Cat# 301870025
Series S CM5 chip Cytiva Cat# BR100530
HEPES Sigma Cat# H3375
Sodium Chloride Thermo Scientific Cat# S271-10
Tween-20 Sigma Cat# P7949
BSA Sigma Cat# A7906
His Capture kit Cytiva Cat# 28995056
Phosphoric acid Sigma Cat# 345245

Critical commercial assays

FuGENE 6 Promega Cat# E2691
Strep-Tactin XT Superflow 50% Zymo research Cat#P2004-1-5
Sensor Chip CM5 Cytiva Cat#BR100030
His Capture Kit Cytiva Cat#28995056
Glycine 1.5 Cytiva Cat# BR100354
HBS-EP+ Buffer Cytiva Cat# BR100826
Spin Miniprep Kit QIAGEN Cat# 27106
Hispeed Plasmid Maxi Kit QIAGEN Cat# 12663
HisTrap Fast Flow GE Healthcare Cat# 17-0921-09
Superdex 200 Increase 10/300 GL Cytiva Cat# 28990945
HRV3C protease Thermo Scientific Cat# PI88946
Pierce™ Fab Preparation Kit Thermo Scientific Cat# 44985
EndoHf NEB Cat# P0703S
Tris Base Thermo Scientific Cat# BP152-10
Calcium acetate Sigma Cat# 114460-21-8
Sodium Cacodylate Hampton research Cat# HR2-575
Glycerol Hampton research Cat# HR2-623
PEG 8000 Sigma Cat# 25322-68-3

Experimental models: Cell lines

Vero E6 ATCC Cat# CRL-1586
HEK293T/17 ATCC Cat# CRL-11268
FreeStyle 293-F Thermo Scientific Cat# R79007
Expi293F Cells Thermo Scientific Cat# A14635
HEK293S GnTI- ATCC Cat# CRL-3022
I1 mouse hybridoma ATCC Cat# CRL-2700

Recombinant DNA

pCMV3-SARS-CoV-2-spike Dr. Peihui Wang, Shandong University, China N/A
pα-H vector Laboratory of Daniel Leahy N/A
pVRC8400 vector https://www.addgene.org Cat#63160

Deposited data

Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD) This study PDB: 7L2C
Cryo-EM structure of NTD-directed neutralizing antibody 1-87 in complex with prefusion SARS-CoV-2 spike glycoprotein This study PDB: 7L2D
EMDB: EMD-23125
Cryo-EM structure of NTD-directed neutralizing antibody 4-18 in complex with prefusion SARS-CoV-2 spike glycoprotein This study PDB: 7L2E
EMDB: EMD-23126
Cryo-EM structure of NTD-directed neutralizing antibody 5-24 in complex with prefusion SARS-CoV-2 spike glycoprotein This study PDB: 7L2F
EMDB: EMD-23127
Cryo-EM structure of NTD-directed neutralizing antibody 4-8 in complex with prefusion SARS-CoV-2 spike glycoprotein This study PDB: 7LQV
EMDB: EMD-23489
Cryo-EM structure of NTD-directed neutralizing antibody 2-17 in complex with prefusion SARS-CoV-2 spike glycoprotein This study PDB: 7LQW
EMDB: EMD-23490
Cryo-EM map of NTD-directed neutralizing antibody 1-68 in complex with prefusion SARS-CoV-2 spike glycoprotein This study EMDB: EMD-23150
Cryo-EM map of NTD-directed neutralizing antibody 2-51 in complex with prefusion SARS-CoV-2 spike glycoprotein This study EMDB: EMD-23151

Software and algorithms

AIMLESS Evans and Murshudov, 2013 https://www.mrc-lmb.cam.ac.uk/harry/pre/aimless.html
CCP4 Winn et al., 2011 https://www.ccp4.ac.uk
Coot Emsley and Cowtan, 2004 https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot
cryoSPARC Punjani et al., 2017 https://cryosparc.com
Leginon Suloway et al., 2005 https://sbgrid.org/software/titles/leginon
Molprobity Davis et al., 2004 http://molprobity.biochem.duke.edu
Phaser McCoy, 2007 https://www.phenix-online.org/documentation/reference/phaser.html
Phenix Adams et al., 2010 https://www.phenix-online.org
The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC https://pymol.org/2/support.html#page-top
SAbPred Dunbar et al., 2016 http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred
UCSF Chimera Pettersen et al., 2004 https://www.cgl.ucsf.edu/chimera/
UCSF Chimera X Pettersen et al., 2021 https://www.cgl.ucsf.edu/chimerax/
XDS Kabsch, 2010 https://xds.mr.mpg.de/
GraphPad Prism Software GraphPad Prism Software, Inc. N/A
PDBePISA Krissinel and Henrick, 2007 https://www.ebi.ac.uk/pdbe/pisa/
Scrubber 2.0 BioLogic Software http://www.biologic.com.au/scrubber.html
The PyMol Molecular Graphics System, v1.8.6 Schrödinger, LLC https://pymol.org/2/
IgBLAST-1.16 Ye et al., 2013 https://www.ncbi.nlm.nih.gov/igblast/
IMGT Schramm et al., 2016 http://www.imgt.org/
MUSCLE v3.8.31 Edgar, 2004 https://www.drive5.com/muscle/manual/install.html
SONAR v2.0 Schramm et al., 2016 https://github.com/scharch/sonar/
Python v3.8.3 https://www.python.org/
The R Project for Statistical Computing https://www.r-project.org/
R bio3d package Grant et al., 2006 http://thegrantlab.org/bio3d/
MAFFT Katoh et al., 2002 https://mafft.cbrc.jp/alignment/software/
FreeSASA v2.0.3 Mitternacht, 2016 https://freesasa.github.io/