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Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose 3'-sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AP5 PDB ENTRY 3AP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose 3'-sulfate, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 9% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.46 50.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.376 α = 98.29 b = 65.4 β = 105.43 c = 71.693 γ = 108.55
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4r 2005-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.977980 Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 21.507 94.4 0.055 0.055 1.9 86082 86082 16.622
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.62 91.5 0.121 0.121 5.8 1.9 6209
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3AP5 1.58 21.44 60510 60510 3121 69.81 0.2018 0.19977 0.2101 0.24179 0.2507 RANDOM 15.907
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] 0.35 -0.22 -0.15 -0.7 -0.21 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.921 r_dihedral_angle_4_deg 16.662 r_dihedral_angle_3_deg 12.891 r_dihedral_angle_1_deg 6.665 r_scangle_it 2.914 r_scbond_it 1.841 r_angle_refined_deg 1.423 r_mcangle_it 1.295 r_angle_other_deg 0.798 r_mcbond_it 0.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.921 r_dihedral_angle_4_deg 16.662 r_dihedral_angle_3_deg 12.891 r_dihedral_angle_1_deg 6.665 r_scangle_it 2.914 r_scbond_it 1.841 r_angle_refined_deg 1.423 r_mcangle_it 1.295 r_angle_other_deg 0.798 r_mcbond_it 0.737 r_mcbond_other 0.182 r_chiral_restr 0.176 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4656 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 108
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling