4F94

Structure of the Class D Beta-Lactamase OXA-24 K84D in Acyl-Enzyme Complex with Oxacillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JC7pdb entry 2JC7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52981% (v/v) PEG 400, 1.0 M Ammonium Sulfate, 0.05 M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.1470.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.334α = 90
b = 102.334β = 90
c = 87.444γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-08-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.1APS21-ID-D

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
12.45097.50.15112.37.21830918309
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)
12.42.491000.6153.677.4

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 REPLACEMENTTHROUGHOUTpdb entry 2JC72.430.371725493797.080.179750.177880.21402RANDOM31.724
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]
-1.47-1.472.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.268
r_dihedral_angle_4_deg21.004
r_dihedral_angle_3_deg16.881
r_dihedral_angle_1_deg5.874
r_scangle_it5.487
r_scbond_it3.473
r_mcangle_it2.173
r_angle_refined_deg2.158
r_mcbond_it1.18
r_angle_other_deg0.887
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.268
r_dihedral_angle_4_deg21.004
r_dihedral_angle_3_deg16.881
r_dihedral_angle_1_deg5.874
r_scangle_it5.487
r_scbond_it3.473
r_mcangle_it2.173
r_angle_refined_deg2.158
r_mcbond_it1.18
r_angle_other_deg0.887
r_chiral_restr0.22
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1939
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms48

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling