7DF5

Human Galectin-3 CRD in complex with novel tetrahydropyran-based thiodisaccharide mimic inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7CXA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.1M Tris (pH 7.5-8.5), 0.1M MgCl2, 0.4M NaSCN, 28-35% PEG 4000 or PEG 6000
Crystal Properties
Matthews coefficientSolvent content
1.7429.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.21α = 90
b = 57.34β = 90
c = 62.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.969APS22-ID

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
11.0842.121000.0490.0540.020.999186.956223
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)
11.081.1199.80.820.8890.3410.7646.7

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 REPLACEMENTTHROUGHOUT7CXA1.0831.353291286099.950.14050.1390.1687RANDOM14.735
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]
-0.14-0.080.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.147
r_dihedral_angle_4_deg12.288
r_dihedral_angle_3_deg10.688
r_dihedral_angle_1_deg7.61
r_rigid_bond_restr5.812
r_angle_refined_deg2.216
r_angle_other_deg1.507
r_chiral_restr0.117
r_bond_refined_d0.022
r_gen_planes_refined0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.147
r_dihedral_angle_4_deg12.288
r_dihedral_angle_3_deg10.688
r_dihedral_angle_1_deg7.61
r_rigid_bond_restr5.812
r_angle_refined_deg2.216
r_angle_other_deg1.507
r_chiral_restr0.117
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1106
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing