2P5E

Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native Diagonal Binding Geometry

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	293	85 mM HEPES, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, pH 7.5, VAPOR DIFFUSION, temperature 293K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.002	α = 90
b = 51.771	β = 98.24
c = 118.27	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 4	MIRROR + MONOCHROMATOR	2005-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1		SRS	PX14.1

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	1.887	117					69966

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	2F53	1.89	117.04	66411	3552	97.44	0.18071	0.17777	0.23579	RANDOM	12.457

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]
1.29		1.52	0.3		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.273
r_dihedral_angle_4_deg	10.558
r_dihedral_angle_3_deg	8.812
r_scangle_it	7.091
r_scbond_it	5.409
r_mcangle_it	3.544
r_mcbond_it	3.072
r_dihedral_angle_1_deg	2.817
r_angle_refined_deg	1.173
r_mcbond_other	0.86
r_angle_other_deg	0.71
r_symmetry_hbond_refined	0.318
r_xyhbond_nbd_refined	0.23
r_symmetry_vdw_other	0.226
r_nbd_other	0.213
r_nbd_refined	0.196
r_xyhbond_nbd_other	0.191
r_nbtor_refined	0.187
r_symmetry_vdw_refined	0.185
r_nbtor_other	0.092
r_chiral_restr	0.088
r_metal_ion_refined	0.019
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6568
Nucleic Acid Atoms
Solvent Atoms	739
Heterogen Atoms	93

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing