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Crystal structure of human galectin-3 carbohydrate-recognition domain at 1.35 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 2.07 40.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.315 α = 90 b = 57.602 β = 90 c = 62.22 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 4 2005-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.35 42.26 97.6 0.038 9.7 3.7 28612
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 1.35 1.42 87.3 0.186 4.9
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 (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 1.35 31.36 27116 1459 97.28 0.17022 0.16948 0.1668 0.18441 0.1823 RANDOM 12.931
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] 0.29 -0.19 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.369 r_dihedral_angle_3_deg 11.046 r_dihedral_angle_4_deg 9.198 r_dihedral_angle_1_deg 6.797 r_scangle_it 4.15 r_scbond_it 2.764 r_mcangle_it 2.02 r_mcbond_it 1.408 r_angle_refined_deg 1.294 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.369 r_dihedral_angle_3_deg 11.046 r_dihedral_angle_4_deg 9.198 r_dihedral_angle_1_deg 6.797 r_scangle_it 4.15 r_scbond_it 2.764 r_mcangle_it 2.02 r_mcbond_it 1.408 r_angle_refined_deg 1.294 r_nbtor_refined 0.31 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.089 r_xyhbond_nbd_refined 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 170 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing