8RLT | pdb_00008rlt

TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index 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
3.04	59.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.698	α = 90
b = 155.061	β = 97.043
c = 93.414	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	2.25	79.57	98.6	0.15	0.06	0.998	10.5	7.2		104999

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	2.25	2.29			2.958	1.164	0.493

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.25	79.57	104896	5132	98.48	0.211	0.2094	0.222	0.2521	0.2627	RANDOM	66.902

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]
0.414		2.591	2.06		-3.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.618
r_dihedral_angle_3_deg	15.902
r_lrange_other	11.499
r_lrange_it	11.497
r_dihedral_angle_2_deg	10.497
r_scangle_it	8.776
r_scangle_other	8.775
r_mcangle_it	8.1
r_mcangle_other	8.1
r_dihedral_angle_1_deg	7.833
r_scbond_it	5.857
r_scbond_other	5.853
r_mcbond_it	5.523
r_mcbond_other	5.522
r_angle_refined_deg	1.57
r_angle_other_deg	0.545
r_symmetry_xyhbond_nbd_refined	0.288
r_nbd_refined	0.212
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.182
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.161
r_symmetry_nbd_refined	0.142
r_ncsr_local_group_3	0.114
r_ncsr_local_group_4	0.113
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_2	0.083
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.031
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12808
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms

Software

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