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The crystal structure of Fructosyl amine: oxygen oxidoreductase (Amadoriase I) from Aspergillus fumigatus in complex with the substrate fructosyl lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Sodium citrate 0.1M, 10%Peg4K, 15% 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.51 50.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.171 α = 90 b = 83.197 β = 90 c = 176.065 γ = 90
Symmetry Space Group P 21 21 21
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 PSI PILATUS 6M 2014-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 1.9 47.96 99.3 0.11 12.8 12.8 80799
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 1.9 2 93 0.736 2.6 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4WCT 1.9 47.96 77606 4084 99.46 0.15072 0.14894 0.1619 0.18466 0.1925 RANDOM 24.802
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] 1.57 -0.75 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.807 r_dihedral_angle_4_deg 15.517 r_dihedral_angle_3_deg 14.414 r_long_range_B_refined 8.586 r_long_range_B_other 8.577 r_dihedral_angle_1_deg 7.967 r_scangle_other 6.317 r_scbond_it 4.326 r_scbond_other 4.306 r_mcangle_it 3.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.807 r_dihedral_angle_4_deg 15.517 r_dihedral_angle_3_deg 14.414 r_long_range_B_refined 8.586 r_long_range_B_other 8.577 r_dihedral_angle_1_deg 7.967 r_scangle_other 6.317 r_scbond_it 4.326 r_scbond_other 4.306 r_mcangle_it 3.294 r_mcangle_other 3.29 r_mcbond_it 2.592 r_mcbond_other 2.592 r_angle_refined_deg 0.676 r_angle_other_deg 0.505 r_chiral_restr 0.048 r_gen_planes_refined 0.019 r_bond_refined_d 0.003 r_gen_planes_other 0.002 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6850 Nucleic Acid Atoms Solvent Atoms 618 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing