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The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 ABDC crystals were grown at 23.5 C using the microbatch under-oil method by mixing in a 1:1 ratio, a 10.5 mg mL-1 ABDC solution in 50 mM Na-Acetate (pH 6.0) and 0.1 mM PLP with a solution containing 100 mM MgCl2, 100 mM Tris (pH 8.5), 25% (v/v) PEG 400, 10% (v/v) glycerol, temperature 298K, pH 7
Crystal Properties Matthews coefficient Solvent content 2.38 48.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.453 α = 90 b = 150.453 β = 90 c = 150.453 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD 2007-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.35 106.6 100 0.076 10.6 22531 39.99
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 2.35 2.41 99.2 0.057 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 2.35 106.6 22531 1217 99.9 0.17 0.168 0.169 0.212 0.2102 RANDOM 39.99
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.981 r_dihedral_angle_4_deg 14.799 r_dihedral_angle_3_deg 13.544 r_dihedral_angle_1_deg 5.301 r_scangle_it 4.08 r_scbond_it 2.715 r_mcangle_it 1.452 r_angle_refined_deg 1.102 r_mcbond_it 0.698 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.981 r_dihedral_angle_4_deg 14.799 r_dihedral_angle_3_deg 13.544 r_dihedral_angle_1_deg 5.301 r_scangle_it 4.08 r_scbond_it 2.715 r_mcangle_it 1.452 r_angle_refined_deg 1.102 r_mcbond_it 0.698 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.2 r_nbd_refined 0.187 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_refined 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 3948 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 20
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling