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Crystal structure of the human galectin-3 carbohydrate-recognition domain 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 2NMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 32% PEG 6000, 100mM MgCl2, 10mM beta mercaptoethanol, 100mM Tris-HCL, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.495 α = 90 b = 57.711 β = 90 c = 62.744 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 2024-10-17 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 1.1 30.86 82.25 1 22.46 11.7 44882
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 1.1 1.14 0.98
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 1.1 30.86 42571 2297 82.27 0.17221 0.17144 0.1714 0.18671 0.1866 RANDOM 12.791
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] 0.62 -0.41 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.899 r_dihedral_angle_2_deg 10.126 r_dihedral_angle_1_deg 8.248 r_long_range_B_refined 5.108 r_long_range_B_other 4.949 r_scangle_other 3.607 r_scbond_it 2.444 r_scbond_other 2.443 r_angle_refined_deg 2.074 r_mcangle_other 1.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.899 r_dihedral_angle_2_deg 10.126 r_dihedral_angle_1_deg 8.248 r_long_range_B_refined 5.108 r_long_range_B_other 4.949 r_scangle_other 3.607 r_scbond_it 2.444 r_scbond_other 2.443 r_angle_refined_deg 2.074 r_mcangle_other 1.489 r_mcangle_it 1.487 r_mcbond_it 1.044 r_mcbond_other 1.044 r_angle_other_deg 0.705 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 182 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction