4D4U

Crystal Structure of Fucose binding lectin from Aspergillus Fumigatus (AFL) in complex with LewisY tetrasaccharide.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AGIPDB ENTRY 4AGI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1200 MM CACL2, 25% PEG 4K, 100 MM TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.1643.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.317α = 96.81
b = 47.529β = 100.24
c = 77.365γ = 113.61
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORSMSINGLE 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
11.9942.0196.10.0811.63.11228642
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)
122.188.90.382.9

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 4AGI1.9942.0137163196796.060.171630.169060.22006RANDOM24.816
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]
-0.03-0.04-0.390.060.040.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.519
r_dihedral_angle_3_deg13.354
r_dihedral_angle_4_deg12.33
r_dihedral_angle_1_deg7.52
r_mcangle_it1.852
r_scbond_it1.628
r_angle_refined_deg1.412
r_mcbond_it1.169
r_mcbond_other1.167
r_angle_other_deg0.748
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.519
r_dihedral_angle_3_deg13.354
r_dihedral_angle_4_deg12.33
r_dihedral_angle_1_deg7.52
r_mcangle_it1.852
r_scbond_it1.628
r_angle_refined_deg1.412
r_mcbond_it1.169
r_mcbond_other1.167
r_angle_other_deg0.748
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms4879
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms338

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOSFLMdata scaling
MOLREPphasing