8AIJ

STRUCTURE OF THE LECB LECTIN FROM PSEUDOMONAS AERUGINOSA STRAIN PAO1 IN COMPLEX WITH N-(alpha-L-Fucopyranosyl)benzamide (6)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A3O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.4293.1524% PEG 8K, 1M LiCl and 100 mM sodium acetate pH = 4.4
Crystal Properties
Matthews coefficientSolvent content
2.2144.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.376α = 101.809
b = 51.589β = 99.474
c = 52.604γ = 115.811
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9MCryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors2022-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.9801SOLEILPROXIMA 2

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
11.540.6995.50.0510.0720.0510.99712.93.4211861
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)
11.51.5392.491.530.450.3180.8813.43.3

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5A3O1.540.6961588757195.5070.1420.13830.1688random selection15.5
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]
0.3410.222-0.0380.0970.067-0.542
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.361
r_dihedral_angle_4_deg17.432
r_dihedral_angle_3_deg10.679
r_dihedral_angle_1_deg7.066
r_lrange_other4.748
r_lrange_it4.747
r_scangle_it3.413
r_scangle_other3.412
r_scbond_it2.334
r_scbond_other2.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.361
r_dihedral_angle_4_deg17.432
r_dihedral_angle_3_deg10.679
r_dihedral_angle_1_deg7.066
r_lrange_other4.748
r_lrange_it4.747
r_scangle_it3.413
r_scangle_other3.412
r_scbond_it2.334
r_scbond_other2.334
r_mcangle_it1.907
r_mcangle_other1.907
r_angle_refined_deg1.824
r_angle_other_deg1.609
r_mcbond_it1.319
r_mcbond_other1.314
r_nbd_refined0.252
r_symmetry_nbd_refined0.219
r_nbd_other0.213
r_symmetry_nbd_other0.205
r_symmetry_xyhbond_nbd_refined0.181
r_nbtor_refined0.164
r_xyhbond_nbd_refined0.161
r_symmetry_xyhbond_nbd_other0.103
r_chiral_restr0.095
r_symmetry_nbtor_other0.087
r_metal_ion_refined0.068
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3286
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing