5A3O

Crystal structure of the LecB lectin from Pseudomonas aeruginosa in complex with Methyl 6-(cinnamido)-6-deoxy-alpha-D-mannopyranoside at 1.6 ansgtrom


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZDVPDB ENTRY 3ZDV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.825% PEG 6K, 100MM CITRIC ACID PH 3.8 AND 1L LITHIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.1743.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.954α = 101.8
b = 51.111β = 99.4
c = 52.348γ = 115.95
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2013-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30AESRFBM30A

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
11.61.8596.60.0425.43.9500762
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)
11.61.63900.186.13.7

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 3ZDV1.639.2547532254196.60.168980.16710.20435RANDOM8.769
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]
0.07-0.290.040.040.030.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.017
r_dihedral_angle_4_deg16.805
r_dihedral_angle_3_deg10.151
r_dihedral_angle_1_deg7.111
r_angle_refined_deg1.63
r_angle_other_deg1.189
r_scbond_it0.943
r_mcangle_it0.935
r_mcbond_it0.583
r_mcbond_other0.583
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.017
r_dihedral_angle_4_deg16.805
r_dihedral_angle_3_deg10.151
r_dihedral_angle_1_deg7.111
r_angle_refined_deg1.63
r_angle_other_deg1.189
r_scbond_it0.943
r_mcangle_it0.935
r_mcbond_it0.583
r_mcbond_other0.583
r_chiral_restr0.102
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3303
Nucleic Acid Atoms
Solvent Atoms621
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing