3D39 | pdb_00003d39

The complex between TCR A6 and human Class I MHC HLA-A2 with the modified HTLV-1 TAX (Y5(4-fluoroPhenylalanine)) peptide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	297	TRIS 0.1 M, PEG4000 15%, MgCl2 0.2M, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 224.245	α = 90
b = 48.32	β = 90.51
c = 93.218	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	IMAGE PLATE	MAR scanner 300 mm plate		2005-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97934	APS	23-ID-D

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	2.8	20	92.8	0.1	18.6	3.4	24354	22601	1	1	62

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	2.8	2.9	69		0.281	2.85	2.8	1658

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 (All)	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	1QSE	2.81	20	1	24800	22591	1166	91	0.20479	0.20128	0.2	0.26898	0.25	RANDOM, 5.2% of the data set	66.412

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]
-5.12		1.71	6.39		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.405
r_dihedral_angle_4_deg	21.535
r_dihedral_angle_3_deg	20.929
r_dihedral_angle_1_deg	7.622
r_angle_refined_deg	1.587
r_mcangle_it	1.397
r_scangle_it	1.127
r_mcbond_it	0.826
r_scbond_it	0.696
r_nbtor_refined	0.323

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.405
r_dihedral_angle_4_deg	21.535
r_dihedral_angle_3_deg	20.929
r_dihedral_angle_1_deg	7.622
r_angle_refined_deg	1.587
r_mcangle_it	1.397
r_scangle_it	1.127
r_mcbond_it	0.826
r_scbond_it	0.696
r_nbtor_refined	0.323
r_symmetry_hbond_refined	0.245
r_xyhbond_nbd_refined	0.202
r_nbd_refined	0.125
r_chiral_restr	0.114
r_symmetry_vdw_refined	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6641
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	24

Software

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