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Crystal structure of the human galectin-3 carbohydrate-recognition domain 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 2NM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 35% PEG 6000, 100mM MgCl2, 100mM Tris-HCL, pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.95 36.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.857 α = 90 b = 56.784 β = 90 c = 61.321 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 2025-03-06 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 1.13 30.97 82.3 1 19.9 10.6 39232
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 1.13 1.17 0.476
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 1.13 30.97 37114 2118 82.31 0.17859 0.17743 0.1774 0.19882 0.1989 RANDOM 15.817
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] 0.21 -0.23 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.57 r_dihedral_angle_1_deg 7.544 r_dihedral_angle_2_deg 6.523 r_long_range_B_refined 4.816 r_long_range_B_other 4.635 r_scangle_other 3.545 r_scbond_it 2.384 r_scbond_other 2.382 r_angle_refined_deg 1.913 r_mcangle_other 1.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.57 r_dihedral_angle_1_deg 7.544 r_dihedral_angle_2_deg 6.523 r_long_range_B_refined 4.816 r_long_range_B_other 4.635 r_scangle_other 3.545 r_scbond_it 2.384 r_scbond_other 2.382 r_angle_refined_deg 1.913 r_mcangle_other 1.733 r_mcangle_it 1.731 r_mcbond_it 1.2 r_mcbond_other 1.198 r_angle_other_deg 0.655 r_chiral_restr 0.093 r_bond_refined_d 0.014 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 1108 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction