6GI5 | pdb_00006gi5

Crystal structure of the ferric enterobactin esterase (PfeE) from Pseudomonas aeruginosa in complex with the tris-catechol vector


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION294PEG MME 2000, Sodium acetate, potassium nitrat
Crystal Properties
Matthews coefficientSolvent content
4.874.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.612α = 90
b = 126.612β = 90
c = 293.711γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96862DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.1189.5399.950.1930.99812.225.221976
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.113.1697.011.04580.3732.925.85

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 REPLACEMENTTHROUGHOUT3.1189.5320163110396.720.243790.241590.240.284960.28RANDOM103.487
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]
-0.56-0.561.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.766
r_long_range_B_refined21.002
r_long_range_B_other21.001
r_dihedral_angle_4_deg20.154
r_dihedral_angle_3_deg18.976
r_scangle_other18.657
r_mcangle_it17.193
r_mcangle_other17.19
r_scbond_it13.248
r_scbond_other13.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.766
r_long_range_B_refined21.002
r_long_range_B_other21.001
r_dihedral_angle_4_deg20.154
r_dihedral_angle_3_deg18.976
r_scangle_other18.657
r_mcangle_it17.193
r_mcangle_other17.19
r_scbond_it13.248
r_scbond_other13.247
r_mcbond_it12.515
r_mcbond_other12.513
r_dihedral_angle_1_deg6.988
r_angle_refined_deg1.112
r_angle_other_deg0.703
r_chiral_restr0.071
r_gen_planes_refined0.015
r_bond_refined_d0.014
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms4130
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing