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Galectin-3 in complex with N-[4-O-(beta-d-Galactopyranosyl)-beta-d-glucopyranosyl]-N-(3-carboxyphenyl)acetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ODY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 291 50 mM Potassium bromide, 30% w/v Polyethylene glycol MME 2,000
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.824 α = 90 b = 58.073 β = 90 c = 63.383 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 PILATUS3 6M 2021-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.059 31.118 91.5 0.066 0.997 9.84 3.55 57197
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.059 1.12 79.7 1.171 0.622 1.23 3.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.059 31.118 57197 1716 91.506 0.151 0.1506 0.1633 0.167 0.1752 15.264
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] 0.685 -1.04 0.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.935 r_dihedral_angle_6_deg 15.331 r_lrange_it 13.361 r_lrange_other 13.357 r_dihedral_angle_3_deg 10.241 r_dihedral_angle_1_deg 8.04 r_scangle_it 7.448 r_scangle_other 7.444 r_scbond_it 5.343 r_scbond_other 5.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.935 r_dihedral_angle_6_deg 15.331 r_lrange_it 13.361 r_lrange_other 13.357 r_dihedral_angle_3_deg 10.241 r_dihedral_angle_1_deg 8.04 r_scangle_it 7.448 r_scangle_other 7.444 r_scbond_it 5.343 r_scbond_other 5.28 r_mcangle_other 4.88 r_mcangle_it 4.871 r_rigid_bond_restr 4.165 r_mcbond_it 3.639 r_mcbond_other 3.615 r_angle_refined_deg 1.788 r_angle_other_deg 0.661 r_symmetry_nbd_refined 0.302 r_nbd_refined 0.24 r_symmetry_xyhbond_nbd_refined 0.2 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.177 r_nbd_other 0.165 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1108 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing