4C56 | pdb_00004c56

X-ray structure of the complex between staphylococcal enterotoxin B, T cell receptor and major histocompatibility complex class II

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OGA	PDB ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C
experimental model	PDB	2IAL	PDB ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C
experimental model	PDB	1SEB	PDB ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		8% PEG 20000, 0.1 M SODIUM CITRATE PH 5.5, 0.09 M MAGNESIUM CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.9	58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.35	α = 90
b = 217.65	β = 99.82
c = 101.41	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	CCD	ADSC QUANTUM 315r		2011-10-10	M	SINGLE WAVELENGTH

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

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	2.9	48.7	99	0.08	13.1	3.2		61924		2	82.8

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	2.9	3.06	99.9		0.58	2.3	3.2

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 ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C	2.9	29.23	61848	3134	98.98	0.2338	0.2329	0.25	0.2511	0.26	RANDOM	65.03

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]
-4.7586		-11.4009	5.0533		-0.2947

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.84
t_omega_torsion	1.47
t_angle_deg	0.87
t_bond_d	0.007
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.84
t_omega_torsion	1.47
t_angle_deg	0.87
t_bond_d	0.007
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16279
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	6

Software

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

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.