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Crystal structure of human galectin-3 CRD in complex with Methyl 2-O-(2-nitrobenzoyl)-3-O-(4-methylbenzoyl)-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 1.95 36.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.26 α = 90 b = 57.82 β = 90 c = 61.92 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 2012-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
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 1.58 42.23 99.9 0.062 19.7 7.4 16853
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 1.58 1.63 0.275 6.1
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 1.58 30.96 16238 820 92.937 0.188 0.1864 0.1962 0.2273 0.2268 15.67
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] 0.042 -0.037 -0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.389 r_dihedral_angle_4_deg 21.659 r_dihedral_angle_3_deg 13.618 r_dihedral_angle_1_deg 8.275 r_lrange_it 4.279 r_lrange_other 4.275 r_scangle_it 2.979 r_scangle_other 2.978 r_scbond_it 1.953 r_scbond_other 1.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.389 r_dihedral_angle_4_deg 21.659 r_dihedral_angle_3_deg 13.618 r_dihedral_angle_1_deg 8.275 r_lrange_it 4.279 r_lrange_other 4.275 r_scangle_it 2.979 r_scangle_other 2.978 r_scbond_it 1.953 r_scbond_other 1.952 r_angle_refined_deg 1.758 r_mcangle_it 1.736 r_mcangle_other 1.735 r_angle_other_deg 1.342 r_mcbond_it 1.252 r_mcbond_other 1.242 r_nbd_other 0.277 r_symmetry_xyhbond_nbd_refined 0.23 r_nbd_refined 0.222 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.162 r_symmetry_xyhbond_nbd_other 0.157 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.073 r_chiral_restr_other 0.029 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 135 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing