8RYN | pdb_00008ryn

Structure of S2 TCR in complex with HLA-A*11:01 bound to ELFSYLIEK peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5BRZ
experimental model	PDB	5XOT
experimental model	PDB	1Q94

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Amino acids (0.02 M Sodium Glutamate; 0.02 M Alanine; 0.02 M Glycine; 0.02 M Lysine hydrochloride; 0.02 M Serine), 0.1 M Buffer system 1 (Imidazole; MES monohydrate) pH 6.5, 50 % Precipitant mix 2 (20% v/v Ethylene glycol; 10 % w/v PEG 8000)

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.75	α = 90
b = 48.69	β = 106.39
c = 115.3	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	PIXEL	DECTRIS PILATUS 6M-F		2017-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.97	77.9	99.94	0.097	0.105	0.039	0.999	13.3	7.1		65906

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2	99.94		1.22	1.34	0.545	0.633	1.3	6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.97	77.9	62652	3242	99.92	0.22166	0.22019	0.2294	0.25052	0.2583	RANDOM	40.49

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]
-2.33		-1.2	2.91		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.833
r_dihedral_angle_4_deg	12.52
r_dihedral_angle_3_deg	12.503
r_dihedral_angle_1_deg	6.588
r_long_range_B_refined	5.186
r_long_range_B_other	5.167
r_scangle_other	2.641
r_mcangle_other	2.033
r_mcangle_it	2.031
r_scbond_it	1.64
r_scbond_other	1.64
r_mcbond_it	1.258
r_mcbond_other	1.24
r_angle_refined_deg	1.176
r_angle_other_deg	1.086
r_chiral_restr	0.038
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
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	6466
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms

Software

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