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Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TTPP and 6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9U8Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293 3.7 mg/mL AzcB:AzcC, 2 mM TTPP, 200 mM NaCl, 100 mM CAPS/NaOH (pH 10.5), 20% (w/v) PEG 8,000
Crystal Properties Matthews coefficient Solvent content 3.43 64.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 274.162 α = 90 b = 158.845 β = 99.2 c = 73.869 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 PIXEL DECTRIS EIGER X 4M 2024-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.01800 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.55 48.02 99.8 0.121 0.985 8.8 3.9 194768 33.69
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) Redundancy Number Unique Reflections (All) 1 2.55 2.59 100 0.597 0.826 2.1 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.55 48.02 1.34 194768 3848 97.13 0.192 0.1912 0.1922 0.2278 0.2286 40.07
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 f_dihedral_angle_d 16.7541 f_angle_d 0.573 f_chiral_restr 0.0419 f_plane_restr 0.004 f_bond_d 0.0024
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16291 Nucleic Acid Atoms Solvent Atoms 599 Heterogen Atoms 227
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing