5E89

Crystal structure of Human galectin-3 CRD in complex with 3-fluophenyl-1,2,3-triazolyl thiodigalactoside inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NN8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729331% PEG 6000, 100MM MGCL2, 8MM BETA MERCEPTOETHANOL, 100MM TRIS HCL
Crystal Properties
Matthews coefficientSolvent content
2.2144.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.045α = 90
b = 58.298β = 90
c = 63.728γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDBRUKER SMART 60002009-05-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54184

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.49743.01592.40.0460.050.01718.25.52117321173
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5856.50.3670.3670.3082.121829

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 REPLACEMENTTHROUGHOUT2NN81.543.0119986107392.060.16920.16810.1896RANDOM16.488
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]
0.61-0.56-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.523
r_dihedral_angle_4_deg14.757
r_dihedral_angle_3_deg10.862
r_dihedral_angle_1_deg6.608
r_scangle_it3.068
r_scbond_it1.969
r_angle_refined_deg1.333
r_mcangle_it1.074
r_angle_other_deg0.729
r_mcbond_it0.551
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.523
r_dihedral_angle_4_deg14.757
r_dihedral_angle_3_deg10.862
r_dihedral_angle_1_deg6.608
r_scangle_it3.068
r_scbond_it1.969
r_angle_refined_deg1.333
r_mcangle_it1.074
r_angle_other_deg0.729
r_mcbond_it0.551
r_mcbond_other0.148
r_chiral_restr0.08
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1101
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms46

Software

Software
Software NamePurpose
SAINTdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing