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Crystal structure of the carbohydrate-recognition domain of R144S galectin-3 mutant in apo form
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 293 100 mM MgCl2, 100 mM TRIS pH 8.5, 35% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.01 38.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.067 α = 90 b = 57.229 β = 90 c = 62.192 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 2025-05-26 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 1.2 31.22 89.09 0.999 13.04 11.1 36583
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 1.2 1.243 0.238
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 1.2 31.22 34751 1828 89.2 0.19035 0.18807 0.1972 0.23695 0.2445 RANDOM 14.293
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] -0.11 -0.44 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.998 r_dihedral_angle_2_deg 7.762 r_dihedral_angle_1_deg 7.276 r_long_range_B_refined 5.519 r_long_range_B_other 5.271 r_scangle_other 3.916 r_scbond_it 2.581 r_scbond_other 2.579 r_mcangle_other 1.917 r_mcangle_it 1.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.998 r_dihedral_angle_2_deg 7.762 r_dihedral_angle_1_deg 7.276 r_long_range_B_refined 5.519 r_long_range_B_other 5.271 r_scangle_other 3.916 r_scbond_it 2.581 r_scbond_other 2.579 r_mcangle_other 1.917 r_mcangle_it 1.914 r_angle_refined_deg 1.901 r_mcbond_it 1.326 r_mcbond_other 1.289 r_angle_other_deg 0.64 r_chiral_restr 0.099 r_bond_refined_d 0.011 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 1103 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction