7L0N | pdb_00007l0n

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6M0J	6M0j, 7jx3
experimental model	PDB	7JX3	6M0j, 7jx3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.29	0.3247	0.33	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 R01GM157729.