2NX5 | pdb_00002nx5

Crystal structure of ELS4 TCR bound to HLA-B*3501 presenting EBV peptide EPLPQGQLTAY at 1.7A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZSD	1ZSD, 2NW2
experimental model	PDB	2NW2	1ZSD, 2NW2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	277	0.1M Na Cacodylate (pH6.4), 0.2M CaCl2, 16% PEG 3350, 3% 1,6Hexanediol, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.479	α = 90
b = 118.067	β = 96.04
c = 131.465	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				2005-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7						87783

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1ZSD, 2NW2	2.7	30	87783	4598	93.52	0.27169	0.26876	0.32702	RANDOM	44.267

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]
0.76		0.17	1.64		-2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.788
r_dihedral_angle_3_deg	16.581
r_dihedral_angle_4_deg	15.895
r_dihedral_angle_1_deg	5.246
r_scangle_it	2.731
r_scbond_it	1.806
r_mcangle_it	1.5
r_angle_refined_deg	0.959
r_mcbond_it	0.829
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.188
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26287
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction