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Crystal structure of human galectin-3 carbohydrate-recognising domain at 2.45 angstrom resolution
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 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 2.21 44.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.341 α = 90 b = 58.238 β = 90 c = 63.731 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 MIRRORS 2005-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE
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 2.45 58 98.4 0.048 11.4 3.7 5400
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) 2.45 2.56 84.1 0.187 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1A3K 2.45 42.99 5400 5134 241 97.92 0.16657 0.16332 0.1576 0.23734 0.2238 RANDOM 23.831
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] 0.02 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.734 r_dihedral_angle_3_deg 15.944 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_1_deg 7.063 r_scangle_it 4.373 r_scbond_it 2.528 r_angle_refined_deg 1.688 r_mcangle_it 1.48 r_mcbond_it 1.009 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.734 r_dihedral_angle_3_deg 15.944 r_dihedral_angle_4_deg 15.924 r_dihedral_angle_1_deg 7.063 r_scangle_it 4.373 r_scbond_it 2.528 r_angle_refined_deg 1.688 r_mcangle_it 1.48 r_mcbond_it 1.009 r_nbtor_refined 0.317 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.183 r_symmetry_vdw_refined 0.169 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1108 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection SAINT data reduction LSCALE data scaling AMoRE phasing