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Crystal structure of the complex of galectin-8N-2,6-Anhydro-5-S-(beta-D-galactopyranosyl)-5-thio-D-altritol
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 Galectin-8N 10 mg/mL in PBS (pH 7.4) was mixed 1:1 with reservoir solution containing 0.1 M Trsi/sodium citrate (pH 5.6), 20% (v/v) 2-propanol, 20% (w/v) PEG 4000 and 1 mM ligand.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.052 α = 90 b = 61.774 β = 90 c = 84.958 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 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 1.9 49.96 92 0.037 0.999 21.4 5.2 21211 33.4
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 1.9 1.95 74 0.318 0.9 3.7
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 1.9 49.96 1.35 21172 1047 91.8 0.191 0.1881 0.1888 0.2489 0.2482 39.04
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 17.2872 f_angle_d 0.7801 f_chiral_restr 0.0661 f_plane_restr 0.007 f_bond_d 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2384 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing