7L0N

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.09 M Buffer System 3 pH 8.5 contains Tris (base); BICINE 27% Precipitant Mix 2 contains Ethylene glycol and PEG8000 0.1 M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.76	67.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.98	α = 90
b = 186.58	β = 96.4
c = 194.52	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CMOS	RDI CMOS_8M		2020-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1	ALS	4.2.2

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	2.78	48.95	94.8	0.506	0.545	0.202	0.97	3.3	7.2		131453

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	2.78	2.83	99.8		3.26	3.671	1.641	0.18		4.7

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	6M0j, 7jx3	2.78	48.9	122372	6375	92.9	0.2921	0.2904	0.3247	RANDOM	86.099

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]
-1.9		0.79	4.32		-2.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.543
r_dihedral_angle_3_deg	14.49
r_dihedral_angle_4_deg	13.66
r_dihedral_angle_1_deg	5.361
r_angle_refined_deg	0.668
r_chiral_restr	0.056
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25898
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	347

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	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 R01GM133198.