5MAY

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PA14 IN COMPLEX WITH 2-Thiophenesulfonamide-N-(beta-L-fucopyranosyl methyl)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.829220% PEG6K 0.5M LiCl 0.1M citric acid ph 3.8
Crystal Properties
Matthews coefficientSolvent content
2.0840.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.089α = 90
b = 65.52β = 90
c = 109.173γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97712ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.6538.5998.20.0530.99820.55.74574327.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6882.70.220.8354.12.7

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 REPLACEMENTTHROUGHOUT5a6q1.6538.5943462222198.030.136460.13460.173RANDOM11.838
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]
0.89-0.14-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.067
r_dihedral_angle_4_deg22.133
r_dihedral_angle_3_deg10.649
r_dihedral_angle_1_deg6.655
r_long_range_B_refined4.936
r_long_range_B_other4.398
r_scangle_other2.6
r_angle_other_deg1.871
r_scbond_it1.73
r_scbond_other1.729
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg46.067
r_dihedral_angle_4_deg22.133
r_dihedral_angle_3_deg10.649
r_dihedral_angle_1_deg6.655
r_long_range_B_refined4.936
r_long_range_B_other4.398
r_scangle_other2.6
r_angle_other_deg1.871
r_scbond_it1.73
r_scbond_other1.729
r_angle_refined_deg1.671
r_mcangle_it1.362
r_mcangle_other1.362
r_mcbond_it0.905
r_mcbond_other0.904
r_chiral_restr0.103
r_bond_refined_d0.016
r_bond_other_d0.015
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3282
Nucleic Acid Atoms
Solvent Atoms645
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing