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Crystal structure of human galectin-3 CRD in complex with Methyl 2-O-(3-nitro-benzoyl)-3-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 2.11 41.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.163 α = 90 b = 58.34 β = 90 c = 63.188 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 1.44 42.86 89.5 0.045 21.4 5.7 22158
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 1.44 1.47 0.169 3.3
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 1.444 31.614 22105 1087 89.519 0.182 0.1798 0.188 0.2207 0.2204 15.263
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] 0.139 -0.122 -0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.606 r_dihedral_angle_4_deg 11.732 r_dihedral_angle_3_deg 11.166 r_dihedral_angle_1_deg 7.642 r_lrange_other 4.519 r_lrange_it 4.498 r_scangle_it 3.452 r_scangle_other 3.422 r_scbond_it 2.393 r_scbond_other 2.392
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.606 r_dihedral_angle_4_deg 11.732 r_dihedral_angle_3_deg 11.166 r_dihedral_angle_1_deg 7.642 r_lrange_other 4.519 r_lrange_it 4.498 r_scangle_it 3.452 r_scangle_other 3.422 r_scbond_it 2.393 r_scbond_other 2.392 r_mcangle_other 1.946 r_mcangle_it 1.945 r_angle_refined_deg 1.922 r_angle_other_deg 1.4 r_mcbond_it 1.351 r_mcbond_other 1.348 r_symmetry_xyhbond_nbd_other 0.476 r_nbd_refined 0.249 r_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.166 r_nbd_other 0.163 r_symmetry_xyhbond_nbd_refined 0.147 r_symmetry_nbd_refined 0.09 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.08 r_chiral_restr_other 0.028 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 180 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing