3V05 | pdb_00003v05

2.4 Angstrom Crystal Structure of Superantigen-like Protein from Staphylococcus aureus.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3URY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	295	Protein: 7.4mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen: PACT (D6), 0.1M MMT buffer (pH 9.0), 25% (w/v) PEG 1500., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.64	α = 90
b = 106.504	β = 90
c = 162.085	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		CCD	MARMOSAIC 300 mm CCD	Beryllium lenses	2011-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.4	30	99.9	0.078	21.8	6.6	31397	31397		-3	58.2

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	2.4	2.44	100		0.523	3.6	6.5	1519

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	3URY	2.4	29.67	29519	29519	1569	99.87	0.19809	0.19809	0.19486	0.2	0.25967	0.26	RANDOM	51.916

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]
-1.76			1.46		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.477
r_dihedral_angle_4_deg	11.54
r_dihedral_angle_3_deg	8.522
r_scangle_it	3.309
r_dihedral_angle_1_deg	2.363
r_scbond_it	2.112
r_mcangle_it	1.264
r_angle_refined_deg	1.219
r_angle_other_deg	0.708
r_mcbond_it	0.674

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6357
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	2

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.