2G9H | pdb_00002g9h

Crystal Structure of Staphylococcal Enterotoxin I (SEI) in Complex with a Human MHC class II Molecule

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SXT	1SXT and 1DHL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	10% dioxane, 1.2 mM (NH4)2SO4 and 100 mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.93	68.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.395	α = 90
b = 99.933	β = 92
c = 72.917	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	298	IMAGE PLATE	RIGAKU RAXIS IV	Osmic mirrors	2005-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	40			4.05		72140

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	2.07			0.378		3.93	7089

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 (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	1SXT and 1DHL	2	29.79	69190	2949	100	0.21488	0.21488	0.21327	0.21	0.2524	0.25	RANDOM	34.003

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]
-1.17		-0.06	2.3		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.95
r_dihedral_angle_4_deg	20.833
r_dihedral_angle_3_deg	17.013
r_dihedral_angle_1_deg	6.628
r_scangle_it	2.716
r_scbond_it	1.727
r_angle_refined_deg	1.451
r_mcangle_it	1.113
r_mcbond_it	0.638
r_symmetry_vdw_refined	0.361

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.95
r_dihedral_angle_4_deg	20.833
r_dihedral_angle_3_deg	17.013
r_dihedral_angle_1_deg	6.628
r_scangle_it	2.716
r_scbond_it	1.727
r_angle_refined_deg	1.451
r_mcangle_it	1.113
r_mcbond_it	0.638
r_symmetry_vdw_refined	0.361
r_nbtor_refined	0.312
r_symmetry_hbond_refined	0.253
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.19
r_metal_ion_refined	0.162
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4856
Nucleic Acid Atoms
Solvent Atoms	460
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	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.