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Crystal structure of cupin-domain containing protein (AzcA) forming triazine (6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid) moiety from Streptomyces mobaraensis in complex with manganese and 2,5,6-triaminopyrimidin-4(3H)-one.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9U8N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 7.3 mg/mL AzcA, 1 mM MnCl2, 200 mM calcium acetate, 100 mM imidazole/HCl (pH 8.0), 20% (w/v) PEG 1,000
Crystal Properties Matthews coefficient Solvent content 1.96 37.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.086 α = 90 b = 42.086 β = 90 c = 198.614 γ = 90
Symmetry Space Group P 41 21 2
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 2024-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.01200 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 1.71 42.09 100 0.089 0.999 17.9 14.1 36850 25.08
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 1.71 1.74 100 1.048 0.673 2.2 15.1
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 1.71 41.17 1.34 36850 3579 99.98 0.188 0.184 0.1847 0.2255 0.2262 32.68
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 14.5903 f_angle_d 1.1454 f_chiral_restr 0.0893 f_bond_d 0.0126 f_plane_restr 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1478 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing