3DJD | pdb_00003djd

Crystal structure of the deglycating enzyme fructosamine oxidase from Aspergillus fumigatus (Amadoriase II)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.42930.1 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 coefficientSolvent content
2.1642.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.31α = 90
b = 54.266β = 95.92
c = 106.252γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7536.9699.90.08737.413.385107
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.751.8199.60.6233.912

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.7536.9680816425499.820.169210.167340.16610.204450.203RANDOM18.925
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.372
r_dihedral_angle_4_deg15.316
r_dihedral_angle_3_deg13.409
r_dihedral_angle_1_deg6.1
r_scangle_it3.384
r_scbond_it2.241
r_mcangle_it1.44
r_angle_refined_deg1.367
r_mcbond_it1.029
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.372
r_dihedral_angle_4_deg15.316
r_dihedral_angle_3_deg13.409
r_dihedral_angle_1_deg6.1
r_scangle_it3.384
r_scbond_it2.241
r_mcangle_it1.44
r_angle_refined_deg1.367
r_mcbond_it1.029
r_nbtor_refined0.305
r_nbd_refined0.199
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.129
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms6678
Nucleic Acid Atoms
Solvent Atoms842
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing