5WI3

Structure of Acinetobacter baumannii carbapenemase OXA-239 K82D bound to cefotaxime


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.2298100 mM NaH2PO4, 100 mM citric acid, 200 mM NaCl, 20% PEG 8000, pH 4.2
Crystal Properties
Matthews coefficientSolvent content
2.754.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.095α = 90
b = 143.032β = 90
c = 44.312γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.07814APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.8198.199.90.0840.0460.99813.17.857689
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8111.81799.80.9490.5050.8732.18.2

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 REPLACEMENTTHROUGHOUT4K0X1.8180.954798282799.750.181150.179930.20458RANDOM41.969
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]
1.010.86-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.92
r_dihedral_angle_3_deg12.447
r_dihedral_angle_4_deg8.2
r_long_range_B_refined8.198
r_long_range_B_other8.197
r_scangle_other5.852
r_dihedral_angle_1_deg5.797
r_scbond_it3.882
r_scbond_other3.881
r_mcangle_other3.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.92
r_dihedral_angle_3_deg12.447
r_dihedral_angle_4_deg8.2
r_long_range_B_refined8.198
r_long_range_B_other8.197
r_scangle_other5.852
r_dihedral_angle_1_deg5.797
r_scbond_it3.882
r_scbond_other3.881
r_mcangle_other3.72
r_mcangle_it3.716
r_mcbond_it2.667
r_mcbond_other2.659
r_angle_refined_deg1.653
r_angle_other_deg1.003
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3730
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing