7P93

Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a sulfated ACKR1 N-terminal peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7P8S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293.150.1 M Imidazole.HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.3647.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.967α = 90
b = 71.181β = 90
c = 79.234γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2021-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.96546ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5547.1699.20.99817.53.251899
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.580.622

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7P8S1.5547.1651740266298.80.18240.18120.2037RANDOM38.13
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]
1.0761-6.84265.7665
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.09
t_omega_torsion4.4
t_angle_deg1.16
t_bond_d0.01
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_sum_occupancies
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2369
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing