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Crystal structure of the carbohydrate-recognition domain of R144S Galectin-3 mutant in complex with Methyl 3-O-toluensulfonyl-beta-D-galactopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM MgCl2, 100mM TRIS pH 8.5, 35% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.04 39.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.182 α = 90 b = 57.666 β = 90 c = 62.373 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 100 PIXEL DECTRIS PILATUS 6M 2025-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.4 31.32 92.68 0.999 13.19 8.7 24469
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 0.423
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.4 31.32 23182 1284 92.7 0.18472 0.18243 0.1825 0.22537 0.2255 RANDOM 15.855
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] -0.01 -0.35 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.856 r_dihedral_angle_1_deg 7.58 r_dihedral_angle_2_deg 7.363 r_long_range_B_refined 6.094 r_long_range_B_other 6.069 r_scangle_other 4.77 r_scbond_it 2.945 r_scbond_other 2.943 r_mcangle_other 2.119 r_mcangle_it 2.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.856 r_dihedral_angle_1_deg 7.58 r_dihedral_angle_2_deg 7.363 r_long_range_B_refined 6.094 r_long_range_B_other 6.069 r_scangle_other 4.77 r_scbond_it 2.945 r_scbond_other 2.943 r_mcangle_other 2.119 r_mcangle_it 2.117 r_angle_refined_deg 1.842 r_mcbond_it 1.439 r_mcbond_other 1.437 r_angle_other_deg 0.606 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1103 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction