3HG1 | pdb_00003hg1

Germline-governed recognition of a cancer epitope by an immunodominant human T cell receptor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F53
experimental model	PDB	1AO7
experimental model	PDB	2BCK
experimental model	PDB	2F53

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	293	23% PEG 550 MME, 0.1M TRIS, 15% Glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.898	α = 90
b = 120.898	β = 90
c = 81.98	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4	Mirror	2007-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.979	SRS	PX14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	48.65	99.6	0.164	0.164	4.512	3.4		23764			65.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.16	100		0.737	0.737	1	3.4	3464

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	3	48.65	23740	1211	99.46	0.229	0.225	0.2327	0.304	0.3057	RANDOM	42.638

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]
1.3			1.3		-2.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.476
r_dihedral_angle_3_deg	8.917
r_dihedral_angle_4_deg	7.347
r_scangle_it	7.146
r_scbond_it	4.55
r_mcangle_it	3.233
r_dihedral_angle_1_deg	2.05
r_mcbond_it	1.769
r_angle_refined_deg	1.021
r_angle_other_deg	1.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	17.476
r_dihedral_angle_3_deg	8.917
r_dihedral_angle_4_deg	7.347
r_scangle_it	7.146
r_scbond_it	4.55
r_mcangle_it	3.233
r_dihedral_angle_1_deg	2.05
r_mcbond_it	1.769
r_angle_refined_deg	1.021
r_angle_other_deg	1.016
r_chiral_restr	0.074
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6583
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	22

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.