4EUP | pdb_00004eup

The complex between TCR JKF6 and human Class I MHC HLA-A2 presenting the MART-1(27-35)(A27L) peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EUR	PDB ENTRIES 4EUR AND 2GTZ
experimental model	PDB	2GTZ	PDB ENTRIES 4EUR AND 2GTZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1 M Bis-Tris, 16% PEG10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.655	α = 90
b = 53.7	β = 112.46
c = 150.514	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	CCD	ADSC QUANTUM 210r		2010-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.978	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	2.88	20	93.8	0.07	15.9	3.5	40105	37988

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	2.88	2.96	95		0.3	2.5	3.4	2028

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 4EUR AND 2GTZ	2.88	20	37988	2007	92.58	0.23806	0.23499	0.24	0.29488	0.3	RANDOM	52.65

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]
5.23		0.67	-1.42		-3.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.039
r_dihedral_angle_4_deg	18.064
r_dihedral_angle_3_deg	17.196
r_dihedral_angle_1_deg	7.101
r_scangle_it	2.785
r_mcangle_it	1.681
r_scbond_it	1.595
r_angle_refined_deg	1.582
r_mcbond_it	1.027
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.039
r_dihedral_angle_4_deg	18.064
r_dihedral_angle_3_deg	17.196
r_dihedral_angle_1_deg	7.101
r_scangle_it	2.785
r_mcangle_it	1.681
r_scbond_it	1.595
r_angle_refined_deg	1.582
r_mcbond_it	1.027
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13081
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.