5O8P

The crystal structure of DfoA bound to FAD, the desferrioxamine biosynthetic pathway cadaverine monooxygenase from the fire blight disease pathogen Erwinia amylovora


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TLX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.1 M HEPES, 1.45 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
5.6278.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.09α = 90
b = 164.09β = 90
c = 168.54γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.976DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.75117.5799.990.06612.113.160324
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.752.850.67

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4tlx2.75117.5757178307199.990.20130.200090.22398RANDOM44.819
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]
2.622.62-5.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.725
r_dihedral_angle_4_deg18.671
r_dihedral_angle_3_deg15.88
r_long_range_B_refined8.697
r_long_range_B_other8.697
r_dihedral_angle_1_deg6.595
r_scangle_other6.095
r_mcangle_it5.191
r_mcangle_other5.19
r_scbond_it3.804
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.725
r_dihedral_angle_4_deg18.671
r_dihedral_angle_3_deg15.88
r_long_range_B_refined8.697
r_long_range_B_other8.697
r_dihedral_angle_1_deg6.595
r_scangle_other6.095
r_mcangle_it5.191
r_mcangle_other5.19
r_scbond_it3.804
r_scbond_other3.804
r_mcbond_it3.235
r_mcbond_other3.231
r_angle_refined_deg1.434
r_angle_other_deg0.967
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms7044
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing