8RLU | pdb_00008rlu

TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 S3N peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NDQ
experimental model	PDB	5MEN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% (w/v) PEG 3350, 100 mM BIS-TRIS propane pH 8.5, 200 mM sodium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.417	α = 90
b = 147.845	β = 99.026
c = 91.908	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 EIGER2 XE 16M		2022-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

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	2.35	65.51	99.4	0.159	0.065	0.992	9.3	6.9		88665

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	2.35	2.39			1.606	0.758	0.521	0.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.35	65.51	88609	4288	99.293	0.211	0.2083	0.2142	0.2609	0.2675	58.715

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]
-0.466		2.556	0.914		-1.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.764
r_dihedral_angle_6_deg	16.225
r_dihedral_angle_2_deg	12.598
r_lrange_it	12.419
r_lrange_other	12.419
r_scangle_it	9.938
r_scangle_other	9.937
r_mcangle_other	8.962
r_mcangle_it	8.959
r_dihedral_angle_1_deg	7.762
r_scbond_it	6.753
r_scbond_other	6.752
r_mcbond_it	6.276
r_mcbond_other	6.276
r_angle_refined_deg	1.567
r_angle_other_deg	0.529
r_symmetry_xyhbond_nbd_refined	0.293
r_nbd_refined	0.22
r_symmetry_nbd_other	0.208
r_symmetry_nbd_refined	0.197
r_nbd_other	0.187
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.174
r_ncsr_local_group_4	0.14
r_ncsr_local_group_3	0.131
r_ncsr_local_group_1	0.102
r_ncsr_local_group_2	0.096
r_symmetry_nbtor_other	0.089
r_symmetry_xyhbond_nbd_other	0.072
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12872
Nucleic Acid Atoms
Solvent Atoms	237
Heterogen Atoms

Software

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