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Crystal structure of the human galectin-1 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 3OY8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200 mM lithium sulphate, 100mM TRIS pH 8.5, PEG 3350 32%, 10mM beta-mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 2.38 48.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.756 α = 90 b = 57.785 β = 90 c = 111.764 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 2025-06-23 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 2 29.61 96.3 0.998 11.6 10.8 19125
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 2 2.071 0.583
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 2 29.61 18158 967 96.48 0.22529 0.2227 0.2284 0.2735 0.2773 RANDOM 27.307
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] 2.59 -2.54 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.451 r_dihedral_angle_1_deg 8.272 r_long_range_B_refined 7.593 r_long_range_B_other 7.592 r_dihedral_angle_2_deg 6.102 r_scangle_other 5.662 r_mcangle_other 4.226 r_mcangle_it 4.222 r_scbond_it 3.605 r_scbond_other 3.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.451 r_dihedral_angle_1_deg 8.272 r_long_range_B_refined 7.593 r_long_range_B_other 7.592 r_dihedral_angle_2_deg 6.102 r_scangle_other 5.662 r_mcangle_other 4.226 r_mcangle_it 4.222 r_scbond_it 3.605 r_scbond_other 3.599 r_mcbond_it 2.695 r_mcbond_other 2.685 r_angle_refined_deg 1.6 r_angle_other_deg 0.561 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 2050 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction