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Crystal structure of the human galectin-1 in complex with p-Methoxyphenyl 3-O-benzyl-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 200mM LiSO4, 100mM Tris-HCl pH 8.5, 35% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.951 α = 90 b = 57.627 β = 90 c = 112.153 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 29.36 92.43 0.997 7.8 7.3 18083
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 2.05 1
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 29.36 17175 903 92.74 0.23082 0.22827 0.2283 0.27907 0.2793 RANDOM 38.833
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] 4.44 -3.7 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.03 r_long_range_B_refined 9.865 r_dihedral_angle_1_deg 8.244 r_dihedral_angle_2_deg 6.477 r_mcangle_it 5.676 r_scbond_it 5.251 r_mcbond_it 3.899 r_angle_refined_deg 2.095 r_chiral_restr 0.136 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.03 r_long_range_B_refined 9.865 r_dihedral_angle_1_deg 8.244 r_dihedral_angle_2_deg 6.477 r_mcangle_it 5.676 r_scbond_it 5.251 r_mcbond_it 3.899 r_angle_refined_deg 2.095 r_chiral_restr 0.136 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other 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 43 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction