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Galectin-8 N-terminal carbohydrate recognition domain in complex with methyl 3-O-((7-carboxy)quinolin-2-yl)-methoxy)-beta-D-galactopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 8 293.5 buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen.
A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).
Crystal Properties Matthews coefficient Solvent content 2.01 38.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.452 α = 90 b = 61.124 β = 90 c = 84.712 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 293.5 PIXEL DECTRIS PILATUS 2M-F 2019-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 49.57 99.8 0.058 16.4 6.5 35999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 1.69
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5GZD 1.6 49.57 35999 1910 99.69 0.1428 0.13924 0.1415 0.21154 0.2126 RANDOM 32.446
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] -1.25 1.37 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.487 r_dihedral_angle_4_deg 19.721 r_dihedral_angle_3_deg 13.579 r_scangle_other 7.847 r_long_range_B_refined 7.821 r_long_range_B_other 7.647 r_dihedral_angle_1_deg 7.598 r_scbond_it 6.517 r_scbond_other 6.517 r_mcangle_it 5.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.487 r_dihedral_angle_4_deg 19.721 r_dihedral_angle_3_deg 13.579 r_scangle_other 7.847 r_long_range_B_refined 7.821 r_long_range_B_other 7.647 r_dihedral_angle_1_deg 7.598 r_scbond_it 6.517 r_scbond_other 6.517 r_mcangle_it 5.735 r_mcangle_other 5.734 r_mcbond_it 5.257 r_mcbond_other 5.255 r_rigid_bond_restr 4.029 r_angle_refined_deg 1.808 r_angle_other_deg 1.359 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2378 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing XDS data reduction XDS data scaling