3KPS

Crystal Structure of the LC13 TCR in complex with HLA B*4405 bound to EEYLQAFTY a self peptide from the ABCD3 protein

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.2M NaOAc, 12-18% PEG 4000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.518	α = 90
b = 54.237	β = 114.43
c = 121.766	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 210r		2008-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	1	Australian Synchrotron	MX1

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	2.7	50	92	0.071	11.7	3.3		21530

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)
	2.7	2.8	55.6		0.295		2	1278

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	PDB ENTRIES 1SYV and 1KGC	2.7	50	21528	1112	91.36	0.197	0.193	0.269	RANDOM	36.988

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		-3.01	-1.29		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.489
r_dihedral_angle_4_deg	19.099
r_dihedral_angle_3_deg	18.266
r_dihedral_angle_1_deg	6.351
r_scangle_it	5.053
r_scbond_it	3.352
r_mcangle_it	2.06
r_angle_refined_deg	1.202
r_mcbond_it	1.193
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.489
r_dihedral_angle_4_deg	19.099
r_dihedral_angle_3_deg	18.266
r_dihedral_angle_1_deg	6.351
r_scangle_it	5.053
r_scbond_it	3.352
r_mcangle_it	2.06
r_angle_refined_deg	1.202
r_mcbond_it	1.193
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.24
r_symmetry_vdw_refined	0.225
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6657
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.