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Crystal structure of the complex of galectin-8N-TDG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 Galecin-8N 10 mg/mL in PBS (pH 7.4) was mixed 1:1 with reservoir solution containing 0.1 M Tris/sodium citrate (pH 5.6), 20% (v/v) 2- propanol, 20 % (w/v) PEG4000 and 1 mM TDG.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.03 α = 90 b = 39.194 β = 107.483 c = 55.734 γ = 90
Symmetry Space Group C 1 2 1
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 2022-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.71 60 94.2 0.214 0.973 6 6.8 12509 25.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 1.74 84.1 1.306 0.503 2.2 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.71 29.89 1.34 12483 615 93.55 0.2432 0.2407 0.2409 0.2926 0.2913 40.2
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 f_dihedral_angle_d 16.2832 f_angle_d 0.7138 f_chiral_restr 0.0561 f_plane_restr 0.0061 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1175 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing