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Crystal Structure of Oxaloacetate Decarboxylase from Pseudomonas Aeruginosa (PA4872) in complex with oxalate and Mg2+.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 18% 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 coefficient Solvent content 2.81 56.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 260.065 α = 90 b = 83.835 β = 112.14 c = 104.874 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2005-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 47.6 97 0.054 10.9 3.27 164404 159433
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 77.8 0.358 2.1 2.13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.9 47.6 164404 143568 15857 96.97 0.19696 0.1912 0.1966 0.2487 0.1939 RANDOM 34.15
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 -0.65 0.21 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.017 r_dihedral_angle_4_deg 18.305 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 10.019 r_scangle_it 3.826 r_scbond_it 2.455 r_angle_refined_deg 1.61 r_mcangle_it 1.587 r_mcbond_it 0.961 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.017 r_dihedral_angle_4_deg 18.305 r_dihedral_angle_3_deg 15.832 r_dihedral_angle_1_deg 10.019 r_scangle_it 3.826 r_scbond_it 2.455 r_angle_refined_deg 1.61 r_mcangle_it 1.587 r_mcbond_it 0.961 r_nbtor_refined 0.301 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_refined 0.162 r_chiral_restr 0.146 r_metal_ion_refined 0.142 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 12897 Nucleic Acid Atoms Solvent Atoms 1859 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling MLPHARE phasing