7Z63

Structure of the LecA lectin from Pseudomonas aeruginosa in complex with a biaryl-thiogalactoside


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5292LecA was dissolved in 20 mM Tris HCl pH 8.0 and 100 mM NaCl to a concentration of 16.9 mgmL and incubated for 3h at room temperature with 3.8 mM of compound. drops were made using the supernatant after centrifugation at 20000 g for 5 minutes since precipitation was observed and a crystallization solution containing 18% PEG3350, 150 mM potassium thiocyanate (KSCN) and 100 mM Tris HCl pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.3146.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.26α = 90
b = 61.932β = 90
c = 180.008γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.97856SOLEILPROXIMA 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
11.75451000.0670.080.0430.99816.16.348775
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)
11.751.7899.90.2910.3470.1860.9765.36.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1OKO1.7543.13148697250699.9380.1640.16130.207413.085
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]
1.1670.827-1.995
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.996
r_dihedral_angle_3_deg12.109
r_dihedral_angle_1_deg6.603
r_dihedral_angle_4_deg5.676
r_lrange_it4.889
r_lrange_other4.306
r_scangle_it3.166
r_scangle_other3.165
r_scbond_other2.158
r_scbond_it2.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.996
r_dihedral_angle_3_deg12.109
r_dihedral_angle_1_deg6.603
r_dihedral_angle_4_deg5.676
r_lrange_it4.889
r_lrange_other4.306
r_scangle_it3.166
r_scangle_other3.165
r_scbond_other2.158
r_scbond_it2.157
r_mcangle_other2.118
r_mcangle_it2.117
r_angle_refined_deg1.809
r_angle_other_deg1.57
r_mcbond_it1.509
r_mcbond_other1.505
r_nbd_refined0.199
r_symmetry_nbd_other0.191
r_nbd_other0.188
r_symmetry_xyhbond_nbd_refined0.177
r_nbtor_refined0.174
r_symmetry_nbd_refined0.166
r_xyhbond_nbd_refined0.147
r_metal_ion_refined0.117
r_chiral_restr0.094
r_symmetry_nbtor_other0.086
r_symmetry_xyhbond_nbd_other0.065
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3602
Nucleic Acid Atoms
Solvent Atoms833
Heterogen Atoms133

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing