4WCT | pdb_00004wct

The crystal structure of Fructosyl amine: oxygen oxidoreductase (Amadoriase I) from Aspergillus fumigatus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DJD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298Sodium citrate 0.1M, 10% PEG 4000, 15% 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.5251.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.396α = 90
b = 83.1β = 90
c = 176.815γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6748.0798.8528.945.6119826
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)
11.671.76950.4733.46.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3DJD1.6748.07113833599398.850.140830.139360.150.168660.18RANDOM16.772
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.686
r_dihedral_angle_4_deg14.997
r_dihedral_angle_3_deg12.659
r_long_range_B_refined7.476
r_dihedral_angle_1_deg7.023
r_long_range_B_other7.021
r_scangle_other5.215
r_scbond_it3.564
r_scbond_other3.564
r_mcangle_other2.702
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6902
Nucleic Acid Atoms
Solvent Atoms1172
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing