7YLB | pdb_00007ylb

Two monobodies recognizing the conserved epitopes of SARS-CoV-2 N antigen applicable to the broad COVID-19 diagnosis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		293.15	0.2M K2SO4, 18% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.081	α = 90
b = 48.458	β = 105.16
c = 143.247	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	PIXEL	DECTRIS PILATUS3 6M		2020-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.979	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.41	138.261	99.8	0.186	7.6	6.6		74632

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.41	2.45			0.945

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	6YUN, 1FNA	2.41	138.261	70911	3709	99.77	0.27	0.2671	0.27	0.3259	0.28	RANDOM	41.358

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]
-2.35		1.52	-4.21		4.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.562
r_dihedral_angle_4_deg	18.856
r_dihedral_angle_3_deg	18.684
r_dihedral_angle_1_deg	7.857
r_angle_refined_deg	1.675
r_chiral_restr	0.132
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9719
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
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.