2WYC

The quorum quenching N-acyl homoserine lactone acylase PvdQ in complex with 3-oxo-lauric acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1924% PEG 6000, 100 MM BICINE PH 9.1
Crystal Properties
Matthews coefficientSolvent content
2.9558.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.8α = 90
b = 166.5β = 90
c = 94.3γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.848.999.90.068.533.6975009221.5
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)
11.921000.362.163.72

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 REPLACEMENTTHROUGHOUT1.94070962375999.690.164260.162940.18985RANDOM26.404
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]
0.180.42-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.034
r_dihedral_angle_4_deg14.92
r_dihedral_angle_3_deg12.288
r_dihedral_angle_1_deg5.519
r_scangle_it2.803
r_scbond_it1.627
r_angle_refined_deg1.121
r_mcangle_it0.875
r_mcbond_it0.462
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.034
r_dihedral_angle_4_deg14.92
r_dihedral_angle_3_deg12.288
r_dihedral_angle_1_deg5.519
r_scangle_it2.803
r_scbond_it1.627
r_angle_refined_deg1.121
r_mcangle_it0.875
r_mcbond_it0.462
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5526
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing