3ZDV

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(2,4,6-trimethylphenylsulfonylamido)-6-deoxy-alpha-D-mannopyranoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DCQPDB ENTRY 3DCQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5330 MM SODIUM CACODYLATE PH 6.5 200 MM AMMONIUM SULPHATE 30% PEG8K
Crystal Properties
Matthews coefficientSolvent content
1.8934.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.53α = 90
b = 76.98β = 90
c = 99.66γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MKIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL2012-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
11.4142.2599.80.0719.27.2761022
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)
11.411.4798.80.653.17

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 3DCQ1.4142.2472296380599.780.116140.11460.14529RANDOM13.07
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]
0.140.95-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.613
r_dihedral_angle_4_deg19.432
r_sphericity_free17.879
r_dihedral_angle_3_deg9.818
r_rigid_bond_restr7.724
r_dihedral_angle_1_deg6.692
r_sphericity_bonded4.798
r_scbond_it2.009
r_angle_refined_deg1.651
r_angle_other_deg1.475
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.613
r_dihedral_angle_4_deg19.432
r_sphericity_free17.879
r_dihedral_angle_3_deg9.818
r_rigid_bond_restr7.724
r_dihedral_angle_1_deg6.692
r_sphericity_bonded4.798
r_scbond_it2.009
r_angle_refined_deg1.651
r_angle_other_deg1.475
r_mcangle_it1.27
r_mcbond_it1.135
r_mcbond_other1.135
r_nbd_refined0.261
r_symmetry_vdw_refined0.249
r_symmetry_vdw_other0.216
r_nbd_other0.204
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.115
r_chiral_restr0.104
r_nbtor_other0.084
r_metal_ion_refined0.063
r_symmetry_hbond_refined0.033
r_bond_refined_d0.015
r_bond_other_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.006
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3308
Nucleic Acid Atoms
Solvent Atoms453
Heterogen Atoms123

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing