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Galectin-3 in complex with 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 2NN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1 M Tris-HCl, pH 8.5, 0.2 M MgCl2, and 35% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.08 40.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.92 α = 90 b = 58.09 β = 90 c = 62.48 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 IMAGE PLATE MAR scanner 345 mm plate 2020-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
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 1.8 31.16 99.9 0.997 26.2 4.9 12637
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 1.8 1.84 0.994
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 31.16 11927 674 99.74 0.13822 0.13612 0.1494 0.17595 0.1903 RANDOM 12.706
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] -0.67 -0.08 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.497 r_dihedral_angle_3_deg 11.622 r_dihedral_angle_4_deg 8.963 r_dihedral_angle_1_deg 7.553 r_long_range_B_refined 5.171 r_long_range_B_other 4.82 r_scangle_other 3.444 r_scbond_it 2.217 r_scbond_other 2.215 r_mcangle_other 1.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.497 r_dihedral_angle_3_deg 11.622 r_dihedral_angle_4_deg 8.963 r_dihedral_angle_1_deg 7.553 r_long_range_B_refined 5.171 r_long_range_B_other 4.82 r_scangle_other 3.444 r_scbond_it 2.217 r_scbond_other 2.215 r_mcangle_other 1.875 r_mcangle_it 1.872 r_angle_refined_deg 1.709 r_angle_other_deg 1.356 r_mcbond_it 1.222 r_mcbond_other 1.211 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1108 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling REFMAC phasing