5EXO

Crystal structure of Human galectin-3 CRD in complex with methyl 2-O-acetyl-3-O-(2H-chromene-3-yl-methyl)-a-D-galactopyranoside 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
2.244.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.796α = 90
b = 58.411β = 90
c = 63.928γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDBRUKER SMART 60002010-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEMACSCIENCE1.54184

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
11.50243.122950.0530.0570.01916.35.22156321563
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)
11.51.5865.70.2570.2570.22631.62108

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 REPLACEMENTTHROUGHOUT2nn81.50243.1220351110094.710.15860.15680.1928RANDOM17.641
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]
0.58-0.43-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.912
r_dihedral_angle_4_deg13.886
r_dihedral_angle_3_deg10.452
r_dihedral_angle_1_deg6.804
r_scangle_it5.525
r_scbond_it3.591
r_mcangle_it3.185
r_mcbond_it1.915
r_angle_refined_deg1.42
r_angle_other_deg0.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.912
r_dihedral_angle_4_deg13.886
r_dihedral_angle_3_deg10.452
r_dihedral_angle_1_deg6.804
r_scangle_it5.525
r_scbond_it3.591
r_mcangle_it3.185
r_mcbond_it1.915
r_angle_refined_deg1.42
r_angle_other_deg0.805
r_mcbond_other0.454
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms164
Heterogen Atoms29

Software

Software
Software NamePurpose
SAINTdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building