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Crystal structure of Human galectin-3 CRD in complex with 3-fluophenyl-1,2,3-triazolyl thiodigalactoside inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 31% PEG 6000, 100MM MGCL2, 8MM BETA MERCEPTOETHANOL, 100MM TRIS HCL
Crystal Properties Matthews coefficient Solvent content 2.21 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.045 α = 90 b = 58.298 β = 90 c = 63.728 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD BRUKER SMART 6000 2009-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54184
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.497 43.015 92.4 0.046 0.05 0.017 18.2 5.5 21173 21173
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) Redundancy Number Unique Reflections (All) 1 1.5 1.58 56.5 0.367 0.367 0.308 2.1 2 1829
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2NN8 1.5 43.01 19986 1073 92.06 0.1692 0.1681 0.1679 0.1896 0.1856 RANDOM 16.488
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.523 r_dihedral_angle_4_deg 14.757 r_dihedral_angle_3_deg 10.862 r_dihedral_angle_1_deg 6.608 r_scangle_it 3.068 r_scbond_it 1.969 r_angle_refined_deg 1.333 r_mcangle_it 1.074 r_angle_other_deg 0.729 r_mcbond_it 0.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.523 r_dihedral_angle_4_deg 14.757 r_dihedral_angle_3_deg 10.862 r_dihedral_angle_1_deg 6.608 r_scangle_it 3.068 r_scbond_it 1.969 r_angle_refined_deg 1.333 r_mcangle_it 1.074 r_angle_other_deg 0.729 r_mcbond_it 0.551 r_mcbond_other 0.148 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1101 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 46
Software Software Software Name Purpose SAINT data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing