5O8R

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.1 M HEPES, 1.3 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
5.5877.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.937α = 90
b = 163.937β = 90
c = 166.73γ = 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 I040.987DiamondI04

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
12.847.5999.810.14616.38.856459
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)
12.82.871.2952

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.847.5953499289599.820.190010.187320.23969RANDOM61.969
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]
0.210.21-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.212
r_dihedral_angle_4_deg21.789
r_dihedral_angle_3_deg18.808
r_long_range_B_other13.7
r_long_range_B_refined13.694
r_scangle_other9.914
r_mcangle_it7.915
r_mcangle_other7.915
r_dihedral_angle_1_deg7.594
r_scbond_it6.475
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.212
r_dihedral_angle_4_deg21.789
r_dihedral_angle_3_deg18.808
r_long_range_B_other13.7
r_long_range_B_refined13.694
r_scangle_other9.914
r_mcangle_it7.915
r_mcangle_other7.915
r_dihedral_angle_1_deg7.594
r_scbond_it6.475
r_scbond_other6.475
r_mcbond_it5.245
r_mcbond_other5.232
r_angle_refined_deg2.122
r_angle_other_deg1.166
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms7036
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms202

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing