3R8B | pdb_00003r8b

Crystal structure of Staphylococcal Enterotoxin B in complex with an affinity matured mouse TCR VBeta8.2 protein, G5-8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3SEB	PDB ENTRIES 3SEB AND 2ICW
experimental model	PDB	2ICW	PDB ENTRIES 3SEB AND 2ICW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	294	Gel-filtered SEB/G5-8 complex at 2.5 mg/ml in 100 mM sodium chloride, 50 mM Tris, pH 7.5. 1:1 protein to reservoir solution containing 6.5% PEG8000, 10 mM zinc sulfate, 100 mM ammonium sulfate, 1% glycerol, 100 mM sodium cacodylate, pH 6.5. Microseeded using crystals grown in same condition without ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.954	α = 90
b = 160.37	β = 90
c = 186.265	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	CCD	ADSC QUANTUM 270	TOROIDAL FOCUSING MIRROR	2010-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A		NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.95	121.531	94.7	0.199	16.75	13.9	69820	66122		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.06	99		0.793	4.5	13.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 3SEB AND 2ICW	2.95	46.57	66380	61375	3244	92.46	0.24705	0.24705	0.24607	0.24	0.26547	0.26	RANDOM	37.936

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]
-1.56			0.93		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.167
r_dihedral_angle_4_deg	22.196
r_dihedral_angle_3_deg	16.7
r_dihedral_angle_1_deg	6.41
r_scangle_it	2.119
r_angle_refined_deg	1.259
r_scbond_it	1.222
r_mcangle_it	1.009
r_angle_other_deg	0.852
r_mcbond_it	0.518

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.167
r_dihedral_angle_4_deg	22.196
r_dihedral_angle_3_deg	16.7
r_dihedral_angle_1_deg	6.41
r_scangle_it	2.119
r_angle_refined_deg	1.259
r_scbond_it	1.222
r_mcangle_it	1.009
r_angle_other_deg	0.852
r_mcbond_it	0.518
r_mcbond_other	0.08
r_chiral_restr	0.07
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21868
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	43

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.