6N9R

Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-AHL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6N9I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292Concentrated protein samples 10mg.mL-1, ammonium sulfate 1 to 2.25M, 0.1M sodium acetate. Soaking in 20 mM of C12 AHL for 5 min. Diffraction quality crystals appeared after 1 d at 292 K
Crystal Properties
Matthews coefficientSolvent content
2.8657.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.01α = 90
b = 108.59β = 115.75
c = 78.6γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03333APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.7570.899.20.0510.0590.99915.213.98109519
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8599.50.4190.480.9473.324.07

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 REPLACEMENTTHROUGHOUT6N9I1.7570.8104043547699.330.178940.175970.23481RANDOM23.912
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]
0.1-0.05-0.04-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.538
r_sphericity_free26.558
r_sphericity_bonded15.976
r_dihedral_angle_4_deg14.388
r_dihedral_angle_3_deg13.905
r_rigid_bond_restr10.352
r_scangle_other5.836
r_dihedral_angle_1_deg5.65
r_long_range_B_refined5.257
r_long_range_B_other5.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.538
r_sphericity_free26.558
r_sphericity_bonded15.976
r_dihedral_angle_4_deg14.388
r_dihedral_angle_3_deg13.905
r_rigid_bond_restr10.352
r_scangle_other5.836
r_dihedral_angle_1_deg5.65
r_long_range_B_refined5.257
r_long_range_B_other5.253
r_scbond_it5.044
r_scbond_other5.042
r_mcangle_other3.888
r_mcangle_it3.886
r_mcbond_it3.376
r_mcbond_other3.32
r_angle_other_deg0.987
r_angle_refined_deg0.595
r_chiral_restr0.03
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.002
r_bond_other_d
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6711
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms250

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing