6RP9 | pdb_00006rp9

Crystal structure of the T-cell receptor NYE_S3 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), 3QDJ (chain D) and 5D2N (chain E)
experimental model	PDB	3QDJ	5e00 (chains A and B), 3QDJ (chain D) and 5D2N (chain E)
experimental model	PDB	5D2N	5e00 (chains A and B), 3QDJ (chain D) and 5D2N (chain E)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M ammonium sulphate, 15 % PEG8k, 0.1 M Tris pH7.5

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.57	α = 90
b = 85.61	β = 91.78
c = 171.92	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		2017-09-25	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	3.12	85.61	100	0.117	0.047	0.999	10.99	6.76		52792

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	3.12	3.2	100		0.999	0.567	0.627	1.25	3.97

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), 3QDJ (chain D) and 5D2N (chain E)	3.12	68.01	52792	2717	99.94	0.22481	0.22349	0.23	0.25046	0.25	RANDOM	117.682

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]
-3.55		-2.27	-1.37		5.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.057
r_dihedral_angle_3_deg	12.213
r_dihedral_angle_4_deg	9.839
r_dihedral_angle_1_deg	4.953
r_long_range_B_refined	1.859
r_long_range_B_other	1.859
r_mcangle_it	1.166
r_mcangle_other	1.166
r_angle_refined_deg	0.929
r_angle_other_deg	0.796
r_scangle_other	0.792
r_mcbond_it	0.629
r_mcbond_other	0.629
r_scbond_it	0.418
r_scbond_other	0.418
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
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	16633
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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