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Crystal structure of the human galectin-1 in complex with p-Methoxyphenyl 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 200mM lithium sulphate, 100mM TRIS pH 8.5, PEG3350 35%, 10 mM beta-mercaptoehanol
Crystal Properties Matthews coefficient Solvent content 2.36 47.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.386 α = 90 b = 57.82 β = 90 c = 112.111 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 2024-12-02 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 1.73 34.73 94.56 0.995 6.4 11 28623
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 1.73 1.792 0.41
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 1.73 34.73 27219 1402 94.7 0.22511 0.22313 0.231 0.26397 0.2696 RANDOM 28.138
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] 3.28 -2.51 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.381 r_long_range_B_refined 8.351 r_long_range_B_other 8.336 r_dihedral_angle_1_deg 7.698 r_dihedral_angle_2_deg 7.502 r_scangle_other 5.96 r_mcangle_it 4.37 r_mcangle_other 4.37 r_scbond_it 3.953 r_scbond_other 3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.381 r_long_range_B_refined 8.351 r_long_range_B_other 8.336 r_dihedral_angle_1_deg 7.698 r_dihedral_angle_2_deg 7.502 r_scangle_other 5.96 r_mcangle_it 4.37 r_mcangle_other 4.37 r_scbond_it 3.953 r_scbond_other 3.94 r_mcbond_it 2.782 r_mcbond_other 2.778 r_angle_refined_deg 1.549 r_angle_other_deg 0.547 r_chiral_restr 0.079 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 82 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction