8QFY

Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.2 M calcium acetate, 0.1 M imidazole pH 8.0, 10% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 326.828	α = 90
b = 79.879	β = 96.894
c = 104.073	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 EIGER2 X 16M		2020-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.33	82.9	100	0.121	0.131	0.987	11.3	6.8		114168

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.33	2.37	100		3.209	3.521	0.34		6

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6GH1, 4WW2	2.33	82.9	114144	5685	99.947	0.245	0.2425	0.2886	74.978

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]
-2.741		-2.502	6.869		-3.423

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.324
r_dihedral_angle_4_deg	20.089
r_dihedral_angle_3_deg	17.572
r_lrange_it	12.213
r_lrange_other	12.213
r_mcangle_it	8.545
r_mcangle_other	8.544
r_scangle_it	8.322
r_scangle_other	8.322
r_dihedral_angle_1_deg	7.377
r_mcbond_other	5.65
r_mcbond_it	5.649
r_scbond_it	5.272
r_scbond_other	5.271
r_angle_refined_deg	1.406
r_angle_other_deg	1.153
r_symmetry_nbd_refined	0.286
r_nbd_other	0.264
r_symmetry_xyhbond_nbd_refined	0.208
r_nbd_refined	0.199
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_other	0.134
r_ncsr_local_group_3	0.091
r_ncsr_local_group_1	0.082
r_symmetry_nbtor_other	0.076
r_ncsr_local_group_4	0.066
r_chiral_restr	0.053
r_ncsr_local_group_2	0.035
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12837
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	8

Software

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