7FBK

Crystal structure of SARS-CoV-2 receptor binding domain N501Y mutant in complex with neutralizing nanobody 20G6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7FBJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	70mM Citric acid, 30mM Bis-Tris propane pH 3.4, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.51	α = 90
b = 90.531	β = 90
c = 162.463	γ = 90

Symmetry
Space Group	P 2 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 PILATUS3 6M		2021-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

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	1.9	19.82	99.9	0.073	0.076	0.021	0.999	16.5	12.5		63067

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	1.9	1.94	99.7		0.983	1.046	0.351	0.849		8.7

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	7FBJ	1.9	19.82	59970	3030	99.8	0.1989	0.1969	0.2394	RANDOM	50.554

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]
1.31			-4.86		3.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.997
r_dihedral_angle_4_deg	18.518
r_dihedral_angle_3_deg	16.321
r_dihedral_angle_1_deg	7.987
r_angle_refined_deg	1.906
r_angle_other_deg	1.389
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.997
r_dihedral_angle_4_deg	18.518
r_dihedral_angle_3_deg	16.321
r_dihedral_angle_1_deg	7.987
r_angle_refined_deg	1.906
r_angle_other_deg	1.389
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4866
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	76

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 R01GM157729.