6TRO | pdb_00006tro

Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HUJ	3HUJ, 6AVF, 5e00
experimental model	PDB	6AVF	3HUJ, 6AVF, 5e00
experimental model	PDB	5E00	3HUJ, 6AVF, 5e00

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1 M succinic acid, 0.1 M HEPES pH 7.0, 1 % w/v PEG MME 2k

Crystal Properties
Matthews coefficient	Solvent content
3.51	64.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 220.04	α = 90
b = 220.04	β = 90
c = 96.83	γ = 120

Symmetry
Space Group	P 64 2 2

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		2017-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	67.91	98.6	0.102	0.037	13.5	6.6		27736			85.884

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.05	99.6		1.939	0.687	1.2	6.8

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	3HUJ, 6AVF, 5e00	3	67.91	26360	1355	98.47	0.2162	0.2133	0.2148	0.2702	0.2678	RANDOM	102.286

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]
-1.63	-0.82		-1.63		5.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.229
r_dihedral_angle_4_deg	15.739
r_dihedral_angle_3_deg	15.01
r_dihedral_angle_1_deg	6.799
r_angle_refined_deg	1.203
r_angle_other_deg	1.05
r_chiral_restr	0.037
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6572
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms

Software

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