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Crystal structure of human galectin-3 CRD in complex with diselenodigalactoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 31% PEG6000, 100 mM magnesium chloride, 8 mM BME, 100 mM Tris-HCl, pH 7.0,
Crystal Properties Matthews coefficient Solvent content 2.04 39.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.906 α = 90 b = 58.366 β = 90 c = 63.059 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 2016-07-19 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) CC (Half) 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 1.99 31.55 99.5 0.984 11 6 9155
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 0.969 7.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6B8K 1.99 31.55 9155 458 99.252 0.182 0.1791 0.1866 0.2468 0.2418 18.626
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] 0.015 0.01 -0.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.306 r_dihedral_angle_4_deg 14.558 r_dihedral_angle_3_deg 14.325 r_dihedral_angle_1_deg 8.336 r_lrange_it 4.629 r_lrange_other 4.56 r_scangle_it 3.639 r_scangle_other 3.638 r_scbond_it 2.292 r_scbond_other 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.306 r_dihedral_angle_4_deg 14.558 r_dihedral_angle_3_deg 14.325 r_dihedral_angle_1_deg 8.336 r_lrange_it 4.629 r_lrange_other 4.56 r_scangle_it 3.639 r_scangle_other 3.638 r_scbond_it 2.292 r_scbond_other 2.29 r_mcangle_other 2.172 r_mcangle_it 2.17 r_angle_refined_deg 1.729 r_mcbond_it 1.504 r_mcbond_other 1.5 r_angle_other_deg 1.243 r_symmetry_nbd_refined 0.2 r_nbd_refined 0.191 r_symmetry_nbd_other 0.175 r_nbd_other 0.17 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.121 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.066 r_chiral_restr_other 0.019 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1112 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing