REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
COV2-2499	Zost et al., 2020a	N/A
COV2-2096	Zost et al., 2020a	N/A
COV2-2050	Zost et al., 2020a	N/A
COV2-2479	Zost et al., 2020a	N/A
COV2-2832	Zost et al., 2020a	N/A
COV2-2165	Zost et al., 2020a	N/A
COV2-2094	Zost et al., 2020a	N/A
COV2-2082	Zost et al., 2020a	N/A
COV2-2677	Zost et al., 2020a	N/A
rCR3022	Dingens et al., 2020	N/A
FITC-conjugated chicken anti-cMyc antibody	Immunology Consultants Laboratory, Inc.	Cat# CMYC-45F
PE-conjugated Goat Anti-Human IgG	Jackson Immuno Research Laboratories	Cat# 109-115-098; RRID: AB_2337675
APC-conjugated Goat Anti-Human IgG	Jackson Immuno Research Laboratories	Cat# 109-135-098; RRID: AB_2337690
Bacterial and Virus Strains
VSV-SARS-CoV-2	Case et al., 2020	N/A
K378E VSV-SARS-CoV-2 (COV2-2094 escape mutant)	This paper	N/A
K378N VSV-SARS-CoV-2 (COV2-2094 escape mutant)	This paper	N/A
E484K VSV-SARS-CoV-2 (COV2-2479 and COV2-2050 escape mutant)	This paper	N/A
G446D VSV-SARS-CoV-2 (COV2-2499 escape mutant)	This paper	N/A
Q498R VSV-SARS-CoV-2 (COV2-2499 escape mutant)	This paper	N/A
Chemicals, Peptides, and Recombinant Proteins
SARS-CoV-2 S2Pecto	Zost et al., 2020a	N/A
SARS-CoV-2 S6Pecto	This study	N/A
Biotinylated human ACE2	ACROBiosystems	Cat# AC2-H82E6
PE-conjugated streptavidin	ThermoFisher	Cat# S866
ExpiCHO Expression Medium	ThermoFisher	Cat# A2910001
Avidin–Peroxidase	Sigma	Cat# A3151
1-Step Ultra TMB-ELISA Substrate Solution	ThermoFisher	Cat# 34029
FreeStyle 293 expression medium	ThermoFisher	Cat# 12338002
Fetal Bovine Serum, ultra-low IgG	ThermoFisher	Cat# 16250078
EZ-Link™ NHS-PEG4-Biotin, No-Weigh™ Format	ThermoFisher	Cat# A39259
FabALACTICA® Fab kit	Genovis	Cat# A2-AFK-025
BioLock Biotin Blocking Solution	IBA Lifescience	Cat# 2-0205-050
Uranyl Formate	EMS	Cat# CF400-CU-50
400 mesh copper EM grids	EMS	Cat# 22451
Critical Commercial Assays
Zymoprep Yeast Plasmid Miniprep II	Zymo Research	Cat# D2004
Deposited Data
PacBio CCSs linking variants to barcodes	Starr et al. 2020	NCBI SRA: BioProject PRJNA639956, BioSample: SAMN15295683
Illumina barcode sequencing	This paper	NCBI SRA: BioProject: PRJNA639956, BioSample: SAMN16054076
COV2-2082 Fab complex with SARS-CoV-2 S6Pecto (negative stain EM)	This paper	EMD-22627
COV2-2096 Fab complex with SARS-CoV-2 S2Pecto (negative stain EM)	This paper	EMD-22148
COV2-2165 Fab complex with SARS-CoV-2 S2Pecto (negative stain EM)	Zost et al., 2020a	EMD-21974
COV2-2479 Fab complex with SARS-CoV-2 S6Pecto (negative stain EM)	This paper	EMD-22628
COV2-2832 Fab complex with SARS-CoV-2 S2Pecto (negative stain EM)	This paper	EMD-22149
SARS-CoV-2 spike trimer cryo-EM structure	Walls et al. 2020b	PDB: 6VYB
ACE2-bound RBD crystal structure	Lan et al. 2020	PDB: 6M0J
CR3022-bound RBD crystal structure	Yuan et al. 2020	PDB: 6W41
GISAID EpiCoV SARS-CoV-2 sequence isolates	GISAID	Full list of contributing labs and accessions: https://github.com/jbloomlab/SARS-CoV-2-RBD_MAP_Crowe_antibodies/blob/master/data/GISAID/gisaid_hcov-19_acknowledgement_table_2020_09_06.pdf
Experimental Models: Cell Lines
Monkey: Vero-E6	ATCC	ATCC: CRL-1586, RRID: CVCL_0574
Hamster: ExpiCHO-S	ThermoFisher Scientific	Cat# A29127, RRID: CVCL_5J31
Human: FreeStyle 293-F	ThermoFisher Scientific	Cat# R79007, RRID: CVCL_D603
Human: Embryonic Kidney (HEK293T)	ATCC	ATCC CRL-3216
Human: Embryonic Kidney cells expressing human ACE2 (HEK293T-hACE2)	BEI	BEI NR-52511
Saccharomyces cerevisiae strain AWY101	Wentz and Shusta 2007	AWY101
Recombinant DNA
Plasmid: pETcon_SARS-CoV-2_RBD	Starr et al. 2020	sequence at https://github.com/jbloomlab/SARS-CoV-2-RBD_DMS/tree/master/data/plasmid_maps/2649_pETcon-SARS-CoV-2-RBD-201aa.gb
Plasmid: HDM_Spikedelta21_D614G	Addgene	Addgene #158762
Plasmid: HDM-Hgpm2	BEI	BEI Resources NR-52517
HDM_Spike_RBD_B7-1	Loes et al. 2020	N/A
Plasmid: pTwist-mCis_G1 COV2-2082	Zost et al., 2020a	N/A
Plasmid: pTwist-mCis_G1 COV2-2096	Zost et al., 2020a	N/A
Plasmid: pTwist-mCis_G1 COV2-2165	Zost et al., 2020a	N/A
Plasmid: pTwist-mCis_G1 COV2-2479	Zost et al., 2020a	N/A
Plasmid: pTwist-mCis_G1 COV2-2832	Zost et al., 2020a	N/A
Plasmid: pTwist-mCis_G1 rCR3022	Zost et al., 2020a	N/A
Plasmid: pTwist-CMV S2Pecto	Zost et al., 2020a	N/A
Plasmid: pTwist-CMV S6Pecto	This paper	N/A
Software and Algorithms
dms_variants, version 0.6.0	GitHub	https://jbloomlab.github.io/dms_variants/
dmslogo, version 0.3.2	GitHub	https://jbloomlab.github.io/dmslogo/
dms-view	Hilton et al. 2020	https://dms-view.github.io/docs/
neutcurve	GitHub	https://jbloomlab.github.io/neutcurve/
custom code	This paper	all analyses provided on github: https://github.com/jbloomlab/SARS-CoV-2-RBD_MAP_Crowe_antibodies
RTCA version 2.1.0	Acea Biosciences, Inc	RTCA Software, RRID: SCR_014821
Cryosparc 2.15.0	Punjani et al., 2017	cryoSPARC RRID: SCR_016501
UCSF Chimera 1.14	Pettersen et al., 2004	UCSF Chimera, RRID: SCR_004097
SerialEM 3.7		SerialEM RRID: SCR_017293
Topaz 0.2.3	Bepler et al., 2019, 2020	Topaz
Other
SARS-CoV-2 RBD mutant libraries	Starr et al. 2020	N/A
ÄKTA pure chromatography system	GE Healthcare Life Sciences	N/A
FEI TF20 electron microscope with Gatan US4000 4k × 4k CCD camera	TFS	N/A
Synergy H1 microplate reader	BioTek	N/A
EL406 washer dispenser	BioTek	N/A
Biostack microplate stacker	BioTek	N/A
StrepTrap HP column	GE Healthcare Life Sciences	Cat# 28-9075-48
HisTrap Excel column	GE Healthcare Life Sciences	Cat# 17-3712-06
HiTrap MabSelect™ SuRe 5 mL column	GE Healthcare Life Sciences	Cat# 29-0491-04
TSKgel G4000SWXL column	TOSOH	N/A
xCELLigence RTCA MP analyzer	Acea Biosciences, Inc	N/A
xCELLigence E-Plate 96 PET cell culture plates	Acea Biosciences, Inc	Cat# 300601010