3O13

Crystal structure of a superantigen-like protein (SAV0433) from Staphylococcus aureus MU50 at 2.05 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	1.000000000M NaCitrate, 0.200000000M NaCl, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.161	α = 90
b = 90.804	β = 90
c = 109.129	γ = 90

Symmetry
Space Group	I 2 2 2

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2010-06-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97941,0.97895	SSRL	BL11-1

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	2.05	29.448	98	0.055	11.44			15922		-3	29.753

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	2.05	2.12	94.4		0.517	1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.05	29.448	15922	799	99.13	0.1931	0.1908	0.2396	RANDOM	52.7329

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]
-2.3			-2.66		4.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.154
r_dihedral_angle_4_deg	17.266
r_dihedral_angle_3_deg	11.654
r_scangle_it	7.29
r_dihedral_angle_1_deg	6.135
r_scbond_it	5.178
r_mcangle_it	3.159
r_mcbond_it	1.825
r_angle_refined_deg	1.502
r_angle_other_deg	0.944

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.154
r_dihedral_angle_4_deg	17.266
r_dihedral_angle_3_deg	11.654
r_scangle_it	7.29
r_dihedral_angle_1_deg	6.135
r_scbond_it	5.178
r_mcangle_it	3.159
r_mcbond_it	1.825
r_angle_refined_deg	1.502
r_angle_other_deg	0.944
r_mcbond_other	0.48
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1489
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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 R01GM133198.