6GI2 | pdb_00006gi2

Crystal structure of the ferric enterobactin esterase (pfeE) mutant(S157A) from Pseudomonas aeruginosa in complex with Tris-catechol vector


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GI0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION294PEG MME 2000, Sodium acetate, potassium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.3547.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.794α = 90
b = 76.602β = 90
c = 129.867γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
11.48129.871000.0580.99916.87.295776
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)
11.481.5199.30.7960.8632.27.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6GI01.4965.9890838484999.920.174390.173120.180.198950.21RANDOM26.077
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]
1.76-0.16-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.335
r_dihedral_angle_4_deg18.664
r_dihedral_angle_3_deg13.09
r_long_range_B_refined7.75
r_long_range_B_other7.75
r_dihedral_angle_1_deg6.505
r_scangle_other6.409
r_scbond_it4.278
r_scbond_other4.277
r_mcangle_it4.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.335
r_dihedral_angle_4_deg18.664
r_dihedral_angle_3_deg13.09
r_long_range_B_refined7.75
r_long_range_B_other7.75
r_dihedral_angle_1_deg6.505
r_scangle_other6.409
r_scbond_it4.278
r_scbond_other4.277
r_mcangle_it4.039
r_mcangle_other4.038
r_mcbond_it2.899
r_mcbond_other2.898
r_angle_refined_deg1.423
r_angle_other_deg0.754
r_chiral_restr0.092
r_gen_planes_refined0.014
r_bond_refined_d0.013
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 Atoms4010
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing