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Crystal structure of human galectin-4 C-terminal carbohydrate recognition domain in complex with galactose derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.6 M ammonium sulfate, 4% (v/v) polyethylene glycol (PEG) 400, 0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.15 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.698 α = 90 b = 128.558 β = 101.219 c = 45.891 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2019-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.28 45.01 98.6 0.992 6.8 3.4 23306
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.36 0.766
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YM2 2.28 36.795 23261 1214 98.343 0.2 0.1967 0.202 0.2662 0.2682 36.074
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] 0.023 -0.003 -0.025 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.328 r_dihedral_angle_3_deg 16.936 r_dihedral_angle_4_deg 13.85 r_dihedral_angle_1_deg 8.466 r_lrange_other 6.979 r_lrange_it 6.977 r_scangle_it 4.903 r_scangle_other 4.902 r_mcangle_it 4.445 r_mcangle_other 4.445
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.328 r_dihedral_angle_3_deg 16.936 r_dihedral_angle_4_deg 13.85 r_dihedral_angle_1_deg 8.466 r_lrange_other 6.979 r_lrange_it 6.977 r_scangle_it 4.903 r_scangle_other 4.902 r_mcangle_it 4.445 r_mcangle_other 4.445 r_scbond_it 3.345 r_scbond_other 3.345 r_mcbond_it 3.097 r_mcbond_other 3.097 r_angle_refined_deg 1.692 r_chiral_restr_other 1.527 r_angle_other_deg 1.208 r_symmetry_nbd_refined 0.218 r_nbd_other 0.205 r_nbd_refined 0.198 r_symmetry_nbd_other 0.179 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.139 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4325 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing