9J4S | pdb_00009j4s

Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3REV
experimental model	PDB	8CX4
experimental model	PDB	7LGD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	0.1M Tris-base/hydrochloric acid (pH 7.0), 0.2 M lithium sulfate, and 1.9 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.978	α = 90
b = 93.303	β = 90
c = 261.912	γ = 90

Symmetry
Space Group	P 21 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 EIGER2 S 9M		2024-06-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.9792	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.95	76.1	99.9	0.995	10.9	7.5		48369

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.06			0.687

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.95	76.1	45924	2450	99.97	0.19581	0.19354	0.1944	0.23786	0.2384	RANDOM	44.418

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]
-0.28			3.31		-3.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.041
r_long_range_B_refined	14.102
r_dihedral_angle_2_deg	12.331
r_mcangle_it	7.819
r_dihedral_angle_1_deg	7.104
r_scbond_it	6.749
r_mcbond_it	4.999
r_angle_refined_deg	1.94
r_chiral_restr	0.122
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13246
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing