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The crystal structure of Fructosyl amine: oxygen oxidoreductase (Amadoriase I) from Aspergillus fumigatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DJD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 Sodium citrate 0.1M, 10% PEG 4000, 15% 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.52 51.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.396 α = 90 b = 83.1 β = 90 c = 176.815 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 2014-07-21 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) 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 1.67 48.07 98.85 28.94 5.6 119826
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 1.67 1.76 95 0.473 3.4 6.2
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 3DJD 1.67 48.07 113833 5993 98.85 0.14083 0.13936 0.1542 0.16866 0.1816 RANDOM 16.772
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] 0.58 -0.19 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_4_deg 14.997 r_dihedral_angle_3_deg 12.659 r_long_range_B_refined 7.476 r_dihedral_angle_1_deg 7.023 r_long_range_B_other 7.021 r_scangle_other 5.215 r_scbond_it 3.564 r_scbond_other 3.564 r_mcangle_other 2.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_4_deg 14.997 r_dihedral_angle_3_deg 12.659 r_long_range_B_refined 7.476 r_dihedral_angle_1_deg 7.023 r_long_range_B_other 7.021 r_scangle_other 5.215 r_scbond_it 3.564 r_scbond_other 3.564 r_mcangle_other 2.702 r_mcangle_it 2.701 r_mcbond_it 1.986 r_mcbond_other 1.981 r_angle_refined_deg 1.345 r_angle_other_deg 0.684 r_chiral_restr 0.092 r_gen_planes_refined 0.019 r_bond_refined_d 0.01 r_gen_planes_other 0.001 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 6902 Nucleic Acid Atoms Solvent Atoms 1172 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing