4TW1 | pdb_00004tw1

Crystal structure of the octameric pore complex of the Staphylococcus aureus Bi-component Toxin LukGH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B07	3B07 prepared using CHAINSAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	Drops consisted of 100 nl protein in 20 mM HEPES buffer pH 7.5 and 100 nl reservoir 30 mM MgCl2, 30 mM CaCl2, 0.1 M Na HEPES/MOPS buffer pH 7.5, 12.5 % v/v MPD, 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350. Crystals appeared after 7 days.

Crystal Properties
Matthews coefficient	Solvent content
4.39	71.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.497	α = 90
b = 198.558	β = 103.26
c = 179.535	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	MARMOSAIC 225 mm CCD		2013-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0000	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.8	48.188	97.9	0.16	0.194	0.109	10.1	3.1	222018	222018			56.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	95.4		0.871	0.871	0.591	0.9	3.1	31557

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	3B07 prepared using CHAINSAW	2.8	48	218497	2207	96	0.2387	0.2381	0.25	0.2923	0.3	RANDOM	36.001

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]
4.69		-3.36	-1.99		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.491
r_dihedral_angle_3_deg	20.748
r_dihedral_angle_4_deg	20.721
r_dihedral_angle_1_deg	8.109
r_mcangle_it	3.887
r_scbond_it	2.696
r_mcbond_it	2.318
r_angle_refined_deg	1.796
r_chiral_restr	0.112
r_bond_refined_d	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.491
r_dihedral_angle_3_deg	20.748
r_dihedral_angle_4_deg	20.721
r_dihedral_angle_1_deg	8.109
r_mcangle_it	3.887
r_scbond_it	2.696
r_mcbond_it	2.318
r_angle_refined_deg	1.796
r_chiral_restr	0.112
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37415
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
REFMAC	refinement
XSCALE	data reduction

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.