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Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with Lacto-N-fucopentaose III
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 Lacto-N-fucopentaose III, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.34 47.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.419 α = 90 b = 49.952 β = 90 c = 70.207 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 95 CCD ADSC QUANTUM 210 2006-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000000 Photon Factory AR-NW12A
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 1.33 24.977 98.7 0.041 0.041 7 37685 37685 9.616
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 1.33 1.36 97.4 0.231 0.231 9.4 7.1 2712
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 1.33 24.977 35696 35696 1878 98.34 0.15773 0.15666 0.1659 0.17824 0.1867 RANDOM 8.336
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] 0.45 -0.31 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.565 r_dihedral_angle_4_deg 22.009 r_dihedral_angle_3_deg 10.245 r_dihedral_angle_1_deg 6.84 r_scangle_it 2.284 r_scbond_it 1.481 r_angle_refined_deg 1.242 r_mcangle_it 1.108 r_angle_other_deg 0.749 r_mcbond_it 0.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.565 r_dihedral_angle_4_deg 22.009 r_dihedral_angle_3_deg 10.245 r_dihedral_angle_1_deg 6.84 r_scangle_it 2.284 r_scbond_it 1.481 r_angle_refined_deg 1.242 r_mcangle_it 1.108 r_angle_other_deg 0.749 r_mcbond_it 0.607 r_mcbond_other 0.129 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 1204 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 69
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling