8PU5 | pdb_00008pu5

Crystal structure of the Acyl-CoA dehydrogenase FadE1(PA0506) E441A from Pseudomonas aeruginosa complexed with C16CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6KPT 
experimental modelPDB 6IJC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52980.1M Bis Tris Propane pH 6.5, 0.2M sodium nitrate, 20% w/v PEG 3350, 10% v/v ethylene glycol, 5mM C16CoA
Crystal Properties
Matthews coefficientSolvent content
2.4549.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.955α = 90
b = 92.955β = 90
c = 128.782γ = 120
Symmetry
Space GroupP 31 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2021-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.44128.781000.1940.1970.0310.99911.538.511495615.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.441.461004.4514.5290.8340.30.429.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4480.63109044576799.920.18610.184620.19430.213780.2176RANDOM22.81
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]
-0.32-0.16-0.321.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.731
r_dihedral_angle_4_deg18.008
r_dihedral_angle_3_deg13.711
r_dihedral_angle_1_deg5.931
r_long_range_B_refined5.706
r_long_range_B_other5.596
r_scangle_other4.449
r_scbond_it3.004
r_scbond_other3.003
r_mcangle_it2.289
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.731
r_dihedral_angle_4_deg18.008
r_dihedral_angle_3_deg13.711
r_dihedral_angle_1_deg5.931
r_long_range_B_refined5.706
r_long_range_B_other5.596
r_scangle_other4.449
r_scbond_it3.004
r_scbond_other3.003
r_mcangle_it2.289
r_mcangle_other2.289
r_mcbond_it1.632
r_mcbond_other1.631
r_angle_refined_deg1.629
r_angle_other_deg1.506
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms4563
Nucleic Acid Atoms
Solvent Atoms421
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
xia2data scaling
xia2data reduction