5A6Y

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with mannose-alpha1,3mannoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A6QPDB ENTRY 5A6Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.524% PEG 8K 0.2M AMSO4 0.1M TRIS PH 8.5. 10% GLYCEROL WAS ADDED AS CRYOPROTECTANT
Crystal Properties
Matthews coefficientSolvent content
2.1342.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.979α = 90
b = 49.779β = 93.34
c = 75.438γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.444.5299.40.04213.2768432
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4294.90.185.42.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 5A6Q1.444.5272808401699.270.124570.122450.16328RANDOM9.473
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]
-0.050.05-0.040.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.764
r_sphericity_free17.042
r_dihedral_angle_3_deg10.241
r_dihedral_angle_1_deg6.871
r_dihedral_angle_4_deg5.283
r_sphericity_bonded3.85
r_rigid_bond_restr3.316
r_long_range_B_refined2.342
r_angle_other_deg1.809
r_angle_refined_deg1.795
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.764
r_sphericity_free17.042
r_dihedral_angle_3_deg10.241
r_dihedral_angle_1_deg6.871
r_dihedral_angle_4_deg5.283
r_sphericity_bonded3.85
r_rigid_bond_restr3.316
r_long_range_B_refined2.342
r_angle_other_deg1.809
r_angle_refined_deg1.795
r_long_range_B_other1.728
r_scangle_other1.19
r_scbond_it1.116
r_scbond_other1.116
r_mcangle_it0.984
r_mcangle_other0.984
r_mcbond_it0.854
r_mcbond_other0.854
r_chiral_restr0.113
r_bond_refined_d0.017
r_bond_other_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3268
Nucleic Acid Atoms
Solvent Atoms681
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing