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Crystal structure of the complex of galectin-8N-2,6-anhydro-3-deoxy-3-S-(beta-D-galactopyranosyl)-3-thio-D-glycero-L-altro-heptonamide
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, HANGING DROP 5.6 289 Protein at 10 mg/mL in PBS (pH 7.4) was mixed 1:1 with reservoir solution containing 0.1 M Tris/NaOAc (pH 5.6) 20% (v/v) 2-propanol and 20% PEG 4000.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.482 α = 90 b = 40.201 β = 115.076 c = 69.761 γ = 90
Symmetry Space Group I 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) 0.976 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 1.78 62 99 0.077 0.998 11.5 6.8 14804 -3 32.97
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 1.78 1.82 99 0.803 0.797 2.3 6.8
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 1.78 27.84 1.35 14800 686 98.79 0.1863 0.1847 0.186 0.2211 0.2237 40.92
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 14.6462 f_angle_d 0.8191 f_chiral_restr 0.0657 f_plane_restr 0.0083 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1183 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing