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Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose
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, 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 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.528 α = 98.41 b = 64.888 β = 105.49 c = 71.584 γ = 108.66
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 RIGAKU JUPITER 210 2005-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.92000 SPring-8 BL38B1
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 2.33 59.462 95.5 0.046 0.046 1.9 26924 26924 23.253
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 2.33 2.39 76.3 0.06 0.06 10.7 1.8 1581
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.33 51.33 25610 25610 1313 95.48 0.19364 0.19077 0.2005 0.25138 0.2602 RANDOM 22.209
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] -0.21 -0.59 -0.09 -0.73 -0.26 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.499 r_dihedral_angle_4_deg 15.627 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_1_deg 6.465 r_scangle_it 1.922 r_angle_refined_deg 1.205 r_scbond_it 1.169 r_mcangle_it 0.846 r_angle_other_deg 0.738 r_mcbond_it 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.499 r_dihedral_angle_4_deg 15.627 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_1_deg 6.465 r_scangle_it 1.922 r_angle_refined_deg 1.205 r_scbond_it 1.169 r_mcangle_it 0.846 r_angle_other_deg 0.738 r_mcbond_it 0.45 r_mcbond_other 0.073 r_chiral_restr 0.072 r_bond_refined_d 0.009 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 4683 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 92
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling