6RPA | pdb_00006rpa

Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01-SLLMWITQV

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E00	5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B)
experimental model	PDB	3REV	5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B)
experimental model	PDB	4DZB	5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.02 M sodium/potassium phosphate, 20 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.26	62.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.16	α = 90
b = 84.25	β = 129.81
c = 111.51	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	PIXEL	DECTRIS PILATUS 6M-F		2017-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	2.56	66.51	99.3	0.064	0.025	0.999	17.9	7.66		37679

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	2.56	2.6	99.7		2.07	0.775	0.637	0.96	7.94

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	5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B)	2.56	66.51	37679	1945	99.31	0.25209	0.2499	0.25	0.29324	0.3	RANDOM	80.735

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]
3.15		-3.46	3.12		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.197
r_dihedral_angle_3_deg	14.575
r_dihedral_angle_4_deg	13.361
r_long_range_B_refined	9.727
r_long_range_B_other	9.727
r_dihedral_angle_1_deg	6.076
r_mcangle_it	5.427
r_mcangle_other	5.427
r_scangle_other	4.541
r_mcbond_it	3.256
r_mcbond_other	3.253
r_scbond_it	2.606
r_scbond_other	2.605
r_angle_refined_deg	1.155
r_angle_other_deg	0.846
r_chiral_restr	0.072
r_bond_refined_d	0.008
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	6277
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms

Software

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