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Crystal structure of human Galectin-3 in complex with small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 BUFFER = 0.1M TRIS (7.8), SALT= NASCN;
PRECIPITANT = PEG 6K
Crystal Properties Matthews coefficient Solvent content 1.62 24.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.35 α = 111.12 b = 43.34 β = 105.87 c = 48.15 γ = 90.42
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 2018-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.12 50 85.7 0.037 9.4 1.7 77739
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.15 0.26
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 1.12 37.11 77739 4052 85.87 0.19406 0.19316 0.1947 0.21097 0.2125 RANDOM 15.515
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] -0.1 -0.04 0.03 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.443 r_dihedral_angle_3_deg 14.163 r_dihedral_angle_4_deg 11.371 r_long_range_B_refined 7.924 r_dihedral_angle_1_deg 7.678 r_scbond_it 2.812 r_angle_refined_deg 2.31 r_mcangle_it 2.062 r_mcbond_it 1.565 r_chiral_restr 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.443 r_dihedral_angle_3_deg 14.163 r_dihedral_angle_4_deg 11.371 r_long_range_B_refined 7.924 r_dihedral_angle_1_deg 7.678 r_scbond_it 2.812 r_angle_refined_deg 2.31 r_mcangle_it 2.062 r_mcbond_it 1.565 r_chiral_restr 0.157 r_bond_refined_d 0.026 r_gen_planes_refined 0.015 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 2213 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing