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Crystal structure of human galectin-3 CRD in complex with Methyl 2-O-(2-nitro-4-fluoro)-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 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.258 α = 90 b = 58.22 β = 90 c = 62.723 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 1.48 42.67 87.9 0.059 14.8 5.6 19942
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 1.48 1.51 0.389 1.2 1.4
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 2NMO 1.485 29.127 19892 997 87.983 0.182 0.1799 0.1865 0.2151 0.2206 17.462
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] 0.005 -0.012 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.772 r_dihedral_angle_4_deg 11.349 r_dihedral_angle_3_deg 10.597 r_dihedral_angle_1_deg 7.378 r_lrange_it 4.479 r_lrange_other 4.479 r_scangle_it 3.221 r_scangle_other 3.175 r_scbond_it 2.157 r_scbond_other 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.772 r_dihedral_angle_4_deg 11.349 r_dihedral_angle_3_deg 10.597 r_dihedral_angle_1_deg 7.378 r_lrange_it 4.479 r_lrange_other 4.479 r_scangle_it 3.221 r_scangle_other 3.175 r_scbond_it 2.157 r_scbond_other 2.11 r_angle_refined_deg 1.738 r_mcangle_it 1.708 r_mcangle_other 1.708 r_angle_other_deg 1.347 r_mcbond_it 1.25 r_mcbond_other 1.245 r_symmetry_xyhbond_nbd_other 0.232 r_xyhbond_nbd_refined 0.211 r_nbd_refined 0.21 r_symmetry_nbd_other 0.177 r_nbd_other 0.175 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_nbd_refined 0.093 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.077 r_chiral_restr_other 0.015 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1109 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing