6RPB

Crystal structure of the T-cell receptor NYE_S1 bound to HLA A2*01-SLLMWITQV

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E00	5e00 and 4FTV
experimental model	PDB	4FTV	5e00 and 4FTV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium sulfate, 25 %(w/v) PEG 4000, 0.1 M tri-Sodium citrate pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.342	α = 93.02
b = 77.134	β = 93.45
c = 184.632	γ = 108.16

Symmetry
Space Group	P 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	PIXEL	DECTRIS PILATUS 6M-F		2014-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97626	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.5	73.11	96.9	0.094	0.094	0.971	2.7	1.7		125234

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.56	96		0.41	0.41	0.767	1.1	1.7

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	5e00 and 4FTV	2.5	73.09	125234	6543	96.67	0.25028	0.24911	0.27271	RANDOM	49.569

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]
-0.19	0.95	-0.6	1.44	0.69	-2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.122
r_dihedral_angle_4_deg	15.489
r_dihedral_angle_3_deg	13.466
r_dihedral_angle_1_deg	5.944
r_long_range_B_refined	1.766
r_long_range_B_other	1.754
r_angle_refined_deg	1.098
r_angle_other_deg	0.842
r_mcangle_it	0.65
r_mcangle_other	0.65
r_scangle_other	0.375
r_mcbond_it	0.346
r_mcbond_other	0.346
r_scbond_it	0.191
r_scbond_other	0.191
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	25965
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing