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Galectin-3 carbohydrate recognition domain in complex with thiodigalactoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A3K pdb entry 1A3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 Hanging drops consisting of
equal volumes of protein solution (100 mM lactose in PBS pH 7.5
supplemented with 2 mM CaCl2 and a protein concentration of
10 mg ml
1) and reservoir solution [100 mM Tris HCl,
31%(w/v) PEG 6000, 100 mM MgCl2 and 8 mM -mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.788 α = 90 b = 58.003 β = 90 c = 63.378 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 295 CCD BRUKER SMART 6000 2011-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE 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 1.5 58 95.5 0.04 20.9 5.4 115029 21329 1 1
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 1.5 1.58 84.1 0.142 3.5 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1A3K 1.5 42.79 1 21329 20202 1085 95.14 0.18 0.13609 0.13537 0.1481 0.14938 0.1621 RANDOM 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] 0.77 -0.6 -0.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 9.118 r_dihedral_angle_1_deg 6.752 r_sphericity_bonded 5.214 r_rigid_bond_restr 3.465 r_angle_refined_deg 1.309 r_angle_other_deg 0.782 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 9.118 r_dihedral_angle_1_deg 6.752 r_sphericity_bonded 5.214 r_rigid_bond_restr 3.465 r_angle_refined_deg 1.309 r_angle_other_deg 0.782 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1108 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 28
Software Software Software Name Purpose PROTEUM PLUS data collection AMoRE phasing REFMAC refinement SAINT data reduction SCALA data scaling