7R6W

SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	1.85 M ammonium sulfate, 0.1 M Tris, pH 8.17, 0.8% w/v polyvinyl alcohol, 1% v/v 1-propanol, 0.01 M HEPES, pH 7

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.267	α = 90
b = 239.372	β = 90
c = 129.806	γ = 90

Symmetry
Space Group	C 2 2 2

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		2021-01-14	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	1.83	39.52	99.6	0.085	0.092	0.035	0.999	16.2	6.7		144449

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	1.83	1.86	99.5		2.96	3.199	1.202	0.306		7

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 and homology model of S2X35 Fab	1.83	38.91	135667	7049	98.28	0.2123	0.2113	0.2316	RANDOM	37.283

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]
1.59			-0.13		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.757
r_dihedral_angle_4_deg	16.847
r_dihedral_angle_3_deg	12.067
r_dihedral_angle_1_deg	7.34
r_angle_refined_deg	1.259
r_angle_other_deg	1.154
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	32.757
r_dihedral_angle_4_deg	16.847
r_dihedral_angle_3_deg	12.067
r_dihedral_angle_1_deg	7.34
r_angle_refined_deg	1.259
r_angle_other_deg	1.154
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	8160
Nucleic Acid Atoms
Solvent Atoms	584
Heterogen Atoms	172

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.