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Crystal structure of human galectin-3 CRD in complex with Methyl 2-O-(2-nitro-4-trifluoromethyl-benzoyl)-3-O-toluoyl-b-D-talopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 31% PEG 6000, 100mM MgCl2, 8mM beta mercaptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.191 α = 90 b = 57.769 β = 90 c = 62.533 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 RIGAKU RAXIS IV++ 2016-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 1.487 42.433 88.3 0.055 15 5.6 19606
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 1.49 1.51 0.26 1.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2NMO 1.487 42.433 19510 988 87.899 0.19 0.188 0.2375 0.2511 17.809
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] -0.002 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.154 r_dihedral_angle_4_deg 11.854 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_1_deg 7.691 r_lrange_it 4.53 r_lrange_other 4.528 r_scangle_other 2.984 r_scangle_it 2.974 r_scbond_it 2.011 r_scbond_other 1.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.154 r_dihedral_angle_4_deg 11.854 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_1_deg 7.691 r_lrange_it 4.53 r_lrange_other 4.528 r_scangle_other 2.984 r_scangle_it 2.974 r_scbond_it 2.011 r_scbond_other 1.955 r_mcangle_it 1.857 r_mcangle_other 1.856 r_angle_refined_deg 1.702 r_angle_other_deg 1.343 r_mcbond_it 1.326 r_mcbond_other 1.316 r_symmetry_nbd_refined 0.279 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.21 r_nbd_other 0.196 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.08 r_chiral_restr_other 0.021 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1109 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing