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Crystal structure of mouse 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 32% PEG 4000, 0.1M TRIS(8.0), 0.4M NASCN,
0.1M MGCL2
Crystal Properties Matthews coefficient Solvent content 3.43 64.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.67 α = 90 b = 110.67 β = 90 c = 110.67 γ = 90
Symmetry Space Group I 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2017-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0332 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.97 35 99.9 0.06 24.6 20.1 16076
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.02 0.038
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 1.97 35 15322 754 99.9 0.175 0.173 0.1737 0.215 0.2141 RANDOM 54.74
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.971 r_dihedral_angle_4_deg 19.308 r_dihedral_angle_3_deg 15.129 r_long_range_B_refined 10.307 r_long_range_B_other 10.265 r_scangle_other 9.64 r_dihedral_angle_1_deg 7.833 r_scbond_it 7.027 r_scbond_other 7.021 r_mcangle_it 5.716
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.971 r_dihedral_angle_4_deg 19.308 r_dihedral_angle_3_deg 15.129 r_long_range_B_refined 10.307 r_long_range_B_other 10.265 r_scangle_other 9.64 r_dihedral_angle_1_deg 7.833 r_scbond_it 7.027 r_scbond_other 7.021 r_mcangle_it 5.716 r_mcangle_other 5.713 r_mcbond_it 5.147 r_angle_refined_deg 2.376 r_angle_other_deg 0.829 r_chiral_restr 0.182 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_gen_planes_other 0.001 r_bond_other_d 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_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 98 Heterogen Atoms 38
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PHASER phasing