5K59

Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising antibody


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.2293Drop contained 200 nl Fab-LukGH at 1:1 ratio + 50 nl seed stock + 150 nl reservoir solution [0.3 M NaCl, 26% polyethylene glycol (PEG) 8000, 0.1 M phosphate citrate pH 4.2]. The seed solution was obtained from 40 % PEG 300, 0.1 M phosphate-citrate pH 4.2, 0.3 M NaCl, 20 mM HEPES pH 7.5.
Crystal Properties
Matthews coefficientSolvent content
2.9658.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.79α = 90
b = 160.932β = 101.18
c = 119.484γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDfocusing mirrors2014-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.0000MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.8448.899.30.1080.99310.13.764655
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.842.9192.50.8831.43.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.8448.5461207327799.080.198880.196810.23727RANDOM73.8
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]
1.842.68-5.011.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.006
r_dihedral_angle_3_deg19.678
r_dihedral_angle_4_deg17.018
r_dihedral_angle_1_deg7.829
r_long_range_B_refined5.939
r_long_range_B_other5.939
r_scangle_other4.035
r_mcangle_it3.607
r_mcangle_other3.607
r_scbond_it2.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.006
r_dihedral_angle_3_deg19.678
r_dihedral_angle_4_deg17.018
r_dihedral_angle_1_deg7.829
r_long_range_B_refined5.939
r_long_range_B_other5.939
r_scangle_other4.035
r_mcangle_it3.607
r_mcangle_other3.607
r_scbond_it2.446
r_scbond_other2.445
r_mcbond_it2.197
r_mcbond_other2.197
r_angle_refined_deg1.488
r_angle_other_deg0.843
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15744
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing