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Crystal structure of the deglycating enzyme fructosamine oxidase from Aspergillus fumigatus (Amadoriase II) in complex with FSA
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, fructosyl thioacetate 3 mM, protein solution 15 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.143 α = 90 b = 53.436 β = 113.33 c = 103.297 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 2007-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.08100 NSLS X29A
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 1.6 29.36 91.3 0.104 14.6 6.8 105596
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) 1.6 1.66 52 0.24 3.3 3.3
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 1.6 28.58 100295 5301 91.07 0.17115 0.16976 0.1679 0.19726 0.1943 RANDOM 18.216
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 32.543 r_dihedral_angle_4_deg 14.273 r_dihedral_angle_3_deg 12.232 r_dihedral_angle_1_deg 5.882 r_scangle_it 3.333 r_scbond_it 2.231 r_mcangle_it 1.294 r_angle_refined_deg 1.247 r_mcbond_it 0.957 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.543 r_dihedral_angle_4_deg 14.273 r_dihedral_angle_3_deg 12.232 r_dihedral_angle_1_deg 5.882 r_scangle_it 3.333 r_scbond_it 2.231 r_mcangle_it 1.294 r_angle_refined_deg 1.247 r_mcbond_it 0.957 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.114 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 7018 Nucleic Acid Atoms Solvent Atoms 925 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement