2GJ6 | pdb_00002gj6

The complex between TCR A6 and human Class I MHC HLA-A2 with the modified HTLV-1 TAX (Y5K-4-[3-Indolyl]-butyric acid) peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QSE	PDB ENTRY 1QSE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	297	PEG8000 30%, 0.1 M Sodium Cacodylate, 0.2 M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 223.846	α = 90
b = 49.019	β = 90.34
c = 94.17	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	CUSTOM-MADE		2005-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9829	APS	19-BM

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	2.56	20	0.992	0.092	15.4	3.5	32172	31915	1	1	53

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	2.56	2.71	93.1		0.473	2.2	2.9	2960

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 1QSE	2.56	20	1	33354	30313	1600	95.68	0.20207	0.19949	0.2	0.24988	0.25	RANDOM; 5% of the data set	44.495

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]
-3.43		-0.58	3.87		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.383
r_dihedral_angle_3_deg	20.674
r_dihedral_angle_4_deg	20.061
r_dihedral_angle_1_deg	7.333
r_scangle_it	2.486
r_angle_refined_deg	1.676
r_scbond_it	1.586
r_mcangle_it	0.985
r_mcbond_it	0.565
r_nbtor_refined	0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.383
r_dihedral_angle_3_deg	20.674
r_dihedral_angle_4_deg	20.061
r_dihedral_angle_1_deg	7.333
r_scangle_it	2.486
r_angle_refined_deg	1.676
r_scbond_it	1.586
r_mcangle_it	0.985
r_mcbond_it	0.565
r_nbtor_refined	0.321
r_xyhbond_nbd_refined	0.198
r_symmetry_hbond_refined	0.159
r_nbd_refined	0.128
r_chiral_restr	0.121
r_symmetry_vdw_refined	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6625
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data scaling
MOLREP	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.