7L5T

Crystal Structure of the Oxacillin-hydrolyzing Class D Extended-spectrum Beta-lactamase OXA-14 from Pseudomonas aeruginosa in Complex with Covalently Bound Clavulanic Acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E3U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP292Protein: 8.0 mg/ml, 0.01M Tris pH 8.3; Screen - AmSO4 (F6): 0.1M Bicine pH 9.0, 2.4M Ammonium sulfate; Soak & Cryo: 50mM Clavulanic acid, 2M Lithium sulfate, 10 min
Crystal Properties
Matthews coefficientSolvent content
2.6553.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.94α = 90
b = 95.451β = 90
c = 125.974γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe2020-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim 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
11.88301000.0710.0710.0770.0310.99825.36.248753-325.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.911000.8410.8410.9160.360.8482.86.3

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 REPLACEMENTTHROUGHOUT1E3U1.8829.9146232245799.830.16870.16720.196RANDOM31.172
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]
0.312.16-2.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.311
r_dihedral_angle_4_deg11.927
r_dihedral_angle_3_deg9.87
r_dihedral_angle_1_deg3.753
r_angle_refined_deg1.321
r_angle_other_deg0.373
r_chiral_restr0.066
r_gen_planes_refined0.055
r_gen_planes_other0.05
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.311
r_dihedral_angle_4_deg11.927
r_dihedral_angle_3_deg9.87
r_dihedral_angle_1_deg3.753
r_angle_refined_deg1.321
r_angle_other_deg0.373
r_chiral_restr0.066
r_gen_planes_refined0.055
r_gen_planes_other0.05
r_bond_refined_d0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3902
Nucleic Acid Atoms
Solvent Atoms358
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing