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Galectin-3 carbohydrate recognition domain in complex with thiodigalactoside at 1.8 resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1 M Tris-HCl, pH 8.5, 0.2 M MgCl2, 35% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.04 39.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.969 α = 90 b = 57.35 β = 90 c = 62.225 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 EIGER X 16M 2023-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.8 42.17 96.7 0.967 17.2 5 11982
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 1.8 1.84 0.959
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 1.8 42.17 11009 648 93.7 0.27149 0.26712 0.273 0.34611 0.3515 RANDOM 7.814
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] -0.9 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.565 r_dihedral_angle_4_deg 18.669 r_dihedral_angle_3_deg 13.91 r_dihedral_angle_1_deg 8.058 r_long_range_B_refined 4.068 r_angle_refined_deg 1.651 r_mcangle_it 0.866 r_scbond_it 0.639 r_mcbond_it 0.532 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.565 r_dihedral_angle_4_deg 18.669 r_dihedral_angle_3_deg 13.91 r_dihedral_angle_1_deg 8.058 r_long_range_B_refined 4.068 r_angle_refined_deg 1.651 r_mcangle_it 0.866 r_scbond_it 0.639 r_mcbond_it 0.532 r_chiral_restr 0.107 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d r_angle_other_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 1108 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing