7FIO

LecA from Pseudomonas aeruginosa in complex with a synthetic monovalent galactosidic inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OKO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.229220% PEG6000, 1 M LiCl,100 mM sodium acetate pH 4.2, 5% DMSO containing 1 mM of compound 1
Crystal Properties
Matthews coefficientSolvent content
2.0138.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.597α = 90
b = 52.677β = 90
c = 156.968γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9786SOLEILPROXIMA 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
11.547.3499.80.0890.0940.0290.99913.510.366700
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)
11.51.5399.10.9991.0590.3430.6069.3

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 REPLACEMENTTHROUGHOUT1OKO1.547.3463204341999.650.17830.17650.212RANDOM19.663
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]
-0.421.57-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.575
r_dihedral_angle_4_deg13.482
r_dihedral_angle_3_deg10.633
r_dihedral_angle_1_deg6.755
r_angle_refined_deg1.896
r_angle_other_deg1.543
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.575
r_dihedral_angle_4_deg13.482
r_dihedral_angle_3_deg10.633
r_dihedral_angle_1_deg6.755
r_angle_refined_deg1.896
r_angle_other_deg1.543
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3597
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms159

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing