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Crystal structure of the deglycating enzyme fructosamine oxidase from Aspergillus fumigatus (Amadoriase II)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 0.1 M Hepes pH 7.4, 10 % iso-propanol, 18 % PEG 4000, protein solution 15 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.31 α = 90 b = 54.266 β = 95.92 c = 106.252 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2006-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
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 1.75 36.96 99.9 0.087 37.4 13.3 85107
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) 1.75 1.81 99.6 0.623 3.9 12
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 SAD THROUGHOUT 1.75 36.96 80816 4254 99.82 0.16921 0.16734 0.1661 0.20445 0.203 RANDOM 18.925
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 32.372 r_dihedral_angle_4_deg 15.316 r_dihedral_angle_3_deg 13.409 r_dihedral_angle_1_deg 6.1 r_scangle_it 3.384 r_scbond_it 2.241 r_mcangle_it 1.44 r_angle_refined_deg 1.367 r_mcbond_it 1.029 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.372 r_dihedral_angle_4_deg 15.316 r_dihedral_angle_3_deg 13.409 r_dihedral_angle_1_deg 6.1 r_scangle_it 3.384 r_scbond_it 2.241 r_mcangle_it 1.44 r_angle_refined_deg 1.367 r_mcbond_it 1.029 r_nbtor_refined 0.305 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 6678 Nucleic Acid Atoms Solvent Atoms 842 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing