5O5C

The crystal structure of DfoJ, the desferrioxamine biosynthetic pathway lysine decarboxylase from the fire blight disease pathogen Erwinia amylovora


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QMA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION29355% V/V polipropylene glycol 400
Crystal Properties
Matthews coefficientSolvent content
3.4664.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 269.791α = 90
b = 269.791β = 90
c = 56.194γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R0.987ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim 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
12.174.9699.910.08419.78.1134700
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.150.6333.8

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 REPLACEMENTTHROUGHOUT2QMA2.1233.652534331324399.910.166040.164960.18662RANDOM30.476
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_deg34.567
r_dihedral_angle_4_deg18.11
r_dihedral_angle_3_deg15.595
r_long_range_B_refined6.757
r_long_range_B_other6.757
r_dihedral_angle_1_deg6.684
r_scangle_other4.751
r_mcangle_it3.655
r_mcangle_other3.655
r_scbond_it3.264
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.567
r_dihedral_angle_4_deg18.11
r_dihedral_angle_3_deg15.595
r_long_range_B_refined6.757
r_long_range_B_other6.757
r_dihedral_angle_1_deg6.684
r_scangle_other4.751
r_mcangle_it3.655
r_mcangle_other3.655
r_scbond_it3.264
r_scbond_other3.264
r_mcbond_it2.616
r_mcbond_other2.616
r_angle_refined_deg1.822
r_angle_other_deg1.158
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.009
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 Atoms21713
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing