2X52

CRYSTAL STRUCTURE OF WHEAT GERM AGGLUTININ ISOLECTIN 3 IN COMPLEX WITH A SYNTHETIC DIVALENT CARBOHYDRATE LIGAND


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WGTPDB ENTRY 1WGT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.04 M POTASSIUM PHOSPHATE, 14% PEG 8000, 20% GLYCEROL.
Crystal Properties
Matthews coefficientSolvent content
2.1142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.33α = 90
b = 101.33β = 90
c = 144.92γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.75098.80.112.035.2360413-3
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)
11.71.893.20.462.443.69

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 1WGT1.775.0857320307798.840.158680.158020.1712RANDOM23.958
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]
5.845.84-11.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.375
r_dihedral_angle_3_deg11.435
r_dihedral_angle_4_deg9.582
r_dihedral_angle_1_deg4.325
r_scangle_it1.811
r_scbond_it1.22
r_angle_refined_deg1.036
r_mcangle_it0.701
r_mcbond_it0.383
r_chiral_restr0.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.375
r_dihedral_angle_3_deg11.435
r_dihedral_angle_4_deg9.582
r_dihedral_angle_1_deg4.325
r_scangle_it1.811
r_scbond_it1.22
r_angle_refined_deg1.036
r_mcangle_it0.701
r_mcbond_it0.383
r_chiral_restr0.058
r_gen_planes_refined0.012
r_bond_refined_d0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2330
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms188

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing