9GV6 | pdb_00009gv6

Structure of TCR in complex with peptide-HLA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5E00
experimental model	PDB	4OZI
experimental model	PDB	4QRP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 7.5, and 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.12	α = 90
b = 93.53	β = 90
c = 388.95	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-05-14	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)	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	2.77	90.94	99.62	0.212	0.22	0.057	0.998	8.1	14.4		69770

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	2.77	2.82	94.03		3.438	3.642	1.158	0.366	0.3	9.2

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	2.77	90.94	66086	3484	99.33	0.21976	0.21709	0.237	0.27357	0.2861	RANDOM	108.509

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]
5.4			-0.02		-5.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.404
r_long_range_B_refined	11.065
r_long_range_B_other	11.065
r_dihedral_angle_2_deg	9.41
r_dihedral_angle_1_deg	8.37
r_scangle_other	8.243
r_mcangle_it	7.803
r_mcangle_other	7.802
r_scbond_it	5.186
r_scbond_other	5.186
r_mcbond_it	4.991
r_mcbond_other	4.99
r_angle_refined_deg	1.767
r_angle_other_deg	0.607
r_chiral_restr	0.081
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	13154
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms

Software

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