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Crystal structure of the complex of galectin-8N-Methyl 2,6-anhydro-3-deoxy-3-S-(b-D-galactopyranosyl)-3-thio-D-glycero-L-altro-heptonate
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 7.4 289 galectin-8N at 10mg/mL in PBS buffer was mixed 1:1 with reservoir containing 0.1 M Tris/NaOAc (pH 5.6), 20% (v/v) 2-propanol, 20% PEG 4000.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.699 α = 90 b = 61.8 β = 90 c = 85.101 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 EMBL/DESY, HAMBURG BEAMLINE X13 0.976 EMBL/DESY, HAMBURG X13
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 1.5 45.41 93.3 0.164 0.977 5.9 4.6 42942 -3 27.35
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 1.5 1.53 55.8 0.599 0.517 0.9 1.8
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 1.5 45.41 1.37 42888 2204 93.08 0.1936 0.192 0.194 0.2237 0.2249 35.11
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 16.6182 f_angle_d 0.8855 f_chiral_restr 0.0711 f_plane_restr 0.0076 f_bond_d 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2377 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing