5WIB

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K0X 

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
2.7254.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.398α = 90
b = 144.744β = 90
c = 43.95γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-06-16MSINGLE 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)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
11.86881.381000.0510.99918.7653055
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.8681.8751000.8660.7811.96.1

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 REPLACEMENTTHROUGHOUT4K0X1.8781.3850364261399.830.187920.185820.22843RANDOM47.631
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]
0.880.32-1.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.81
r_dihedral_angle_3_deg13.629
r_dihedral_angle_4_deg10.623
r_dihedral_angle_1_deg7.837
r_long_range_B_refined7.614
r_long_range_B_other7.54
r_scangle_other5.379
r_mcangle_it4.059
r_mcangle_other4.058
r_scbond_other3.794
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.81
r_dihedral_angle_3_deg13.629
r_dihedral_angle_4_deg10.623
r_dihedral_angle_1_deg7.837
r_long_range_B_refined7.614
r_long_range_B_other7.54
r_scangle_other5.379
r_mcangle_it4.059
r_mcangle_other4.058
r_scbond_other3.794
r_scbond_it3.793
r_mcbond_it3.017
r_mcbond_other3.017
r_angle_refined_deg1.231
r_angle_other_deg0.664
r_chiral_restr0.088
r_gen_planes_refined0.02
r_bond_refined_d0.009
r_gen_planes_other0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3743
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing