3B8I

Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629818% PEG 3350, 20% glycerol, 0.1M MES, 10 mg/mL protein in 5mM MgCl2, 5mM oxalate, 10mM Na+Hepes pH 7.0; Crystallization drops contained equal volumes of reservoir solution and protein solution, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8156.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 260.065α = 90
b = 83.835β = 112.14
c = 104.874γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2005-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.947.6970.05410.93.27164404159433
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)
11.91.9777.80.3582.12.13

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.947.61644041435681585796.970.196960.19120.2487RANDOM34.15
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]
-1.78-0.650.211.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_4_deg18.305
r_dihedral_angle_3_deg15.832
r_dihedral_angle_1_deg10.019
r_scangle_it3.826
r_scbond_it2.455
r_angle_refined_deg1.61
r_mcangle_it1.587
r_mcbond_it0.961
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.017
r_dihedral_angle_4_deg18.305
r_dihedral_angle_3_deg15.832
r_dihedral_angle_1_deg10.019
r_scangle_it3.826
r_scbond_it2.455
r_angle_refined_deg1.61
r_mcangle_it1.587
r_mcbond_it0.961
r_nbtor_refined0.301
r_nbd_refined0.209
r_symmetry_hbond_refined0.208
r_xyhbond_nbd_refined0.18
r_symmetry_vdw_refined0.162
r_chiral_restr0.146
r_metal_ion_refined0.142
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms12897
Nucleic Acid Atoms
Solvent Atoms1859
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
MLPHAREphasing