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Co-crystallization of human galectin-3 CRD 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 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 2.05 40.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.933 α = 90 b = 57.929 β = 90 c = 62.067 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 CCD ADSC QUANTUM 210r 2013-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953 Australian Synchrotron MX1
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 1.2 42.35 93.2 0.053 18.4 7 38453
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 1.2 1.22 0.652 1.5
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 1.201 42.349 38398 1856 93.251 0.154 0.1538 0.1616 0.1642 0.1703 11.799
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] 0.156 -0.122 -0.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.652 r_dihedral_angle_4_deg 16.701 r_dihedral_angle_3_deg 10.856 r_dihedral_angle_1_deg 7.877 r_lrange_it 4.755 r_lrange_other 4.753 r_scangle_it 2.989 r_scangle_other 2.985 r_angle_refined_deg 2.017 r_scbond_it 2.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.652 r_dihedral_angle_4_deg 16.701 r_dihedral_angle_3_deg 10.856 r_dihedral_angle_1_deg 7.877 r_lrange_it 4.755 r_lrange_other 4.753 r_scangle_it 2.989 r_scangle_other 2.985 r_angle_refined_deg 2.017 r_scbond_it 2.016 r_scbond_other 2.003 r_angle_other_deg 1.437 r_mcangle_other 1.328 r_mcangle_it 1.326 r_mcbond_it 0.933 r_mcbond_other 0.926 r_symmetry_xyhbond_nbd_refined 0.364 r_xyhbond_nbd_refined 0.226 r_nbd_refined 0.215 r_symmetry_nbd_other 0.18 r_nbd_other 0.177 r_nbtor_refined 0.176 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.081 r_symmetry_nbd_refined 0.063 r_chiral_restr_other 0.02 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 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 219 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing