3ROH | pdb_00003roh

Crystal Structure of Leukotoxin (LukE) from Staphylococcus aureus subsp. aureus COL.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T5R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	Protein: 7mG/mL, 0.25M Sodium chloride, 0.01M Tris, pH 8.3. Screen: JCSG+, D7, 0.2M Lithium sulfate, 0.1M Tris, pH 8.5, 40% v/v PEG 400. VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.904	α = 90
b = 133.904	β = 90
c = 64.473	γ = 90

Symmetry
Space Group	I 4

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 300 mm CCD	Beryllium lenses	2011-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	3.2	30	100	0.077	25.8	7.5	9573	9573		-3	87.7

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	3.2	3.26	100		0.552	4	7.6	467

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	1T5R	3.2	29.94	9098	9098	459	99.94	0.18055	0.18055	0.17845	0.18	0.22418	0.23	RANDOM	107.369

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.219
r_dihedral_angle_4_deg	8.218
r_dihedral_angle_3_deg	7.279
r_scangle_it	3.54
r_scbond_it	2.122
r_mcangle_it	1.573
r_dihedral_angle_1_deg	1.569
r_angle_refined_deg	1.358
r_mcbond_it	0.805
r_angle_other_deg	0.741

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.219
r_dihedral_angle_4_deg	8.218
r_dihedral_angle_3_deg	7.279
r_scangle_it	3.54
r_scbond_it	2.122
r_mcangle_it	1.573
r_dihedral_angle_1_deg	1.569
r_angle_refined_deg	1.358
r_mcbond_it	0.805
r_angle_other_deg	0.741
r_mcbond_other	0.122
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2248
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	12

Software

Software
Software Name	Purpose
Blu-Ice	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.