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Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose sialic acid
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 sialic acid, 50mM sodium chloride, 0.5mM DTT, 80mM ammonium
fluoride, 7.5% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.36 α = 90 b = 49.917 β = 90 c = 70.289 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 315r 2005-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000000 Photon Factory BL-5A
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 1.53 24.961 99.9 0.034 0.034 12.8 25280 25280 14.014
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 1.53 1.57 100 0.192 0.192 12.4 8.5 1826
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 (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 3AP5 1.53 24.96 23937 23937 1282 100 0.16493 0.16493 0.16373 0.1764 0.18828 0.1949 RANDOM 11.776
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] 0.53 -0.13 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.027 r_dihedral_angle_4_deg 19.095 r_dihedral_angle_3_deg 10.596 r_dihedral_angle_1_deg 6.593 r_scangle_it 2.9 r_scbond_it 1.812 r_mcangle_it 1.328 r_angle_refined_deg 1.299 r_angle_other_deg 0.794 r_mcbond_it 0.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.027 r_dihedral_angle_4_deg 19.095 r_dihedral_angle_3_deg 10.596 r_dihedral_angle_1_deg 6.593 r_scangle_it 2.9 r_scbond_it 1.812 r_mcangle_it 1.328 r_angle_refined_deg 1.299 r_angle_other_deg 0.794 r_mcbond_it 0.739 r_mcbond_other 0.155 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1204 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 44
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling