2XNA | pdb_00002xna

Crystal structure of the complex between human T cell receptor and staphylococcal enterotoxin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OGA	PDB ENTRY 1OGA CHAINS D, E AND 1HXY CHAIN D
experimental model	PDB	1HXY	PDB ENTRY 1OGA CHAINS D, E AND 1HXY CHAIN D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		12% W/V PEG 5000 MME, 0.1 M MES PH 6.5, 0.1 M NACL

Crystal Properties
Matthews coefficient	Solvent content
2.9	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.692	α = 90
b = 49.98	β = 131.61
c = 132.834	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC CCD	PT COATED MIRRORS	2010-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.1	45.65	99.4	0.05	15.2	3.8		52446		2	44.39

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.21	99.1		0.4	3.4	3.8

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	PDB ENTRY 1OGA CHAINS D, E AND 1HXY CHAIN D	2.1	99.33	49776	2670	99.16	0.22461	0.22256	0.22	0.26137	0.26	RANDOM	37.705

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]
-1.84		-1.28	0.8		-0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.452
r_dihedral_angle_3_deg	15.927
r_dihedral_angle_4_deg	12.713
r_dihedral_angle_1_deg	6.211
r_scangle_it	2.844
r_scbond_it	1.78
r_mcangle_it	1.417
r_angle_refined_deg	1.293
r_mcbond_it	0.765
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5162
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing