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Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with iodide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.55mM protein, 10mM Hepes-NaOH, 50mM sodium chloride, 0.5mM DTT, 125mM ammonium fluoride, 8% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.78 55.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.591 α = 90 b = 75.869 β = 90 c = 77.901 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 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 1.30000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.947 38.954 99.9 28969 28969
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.94 2.01 99.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.95 38.95 27561 27561 1408 99.51 0.20342 0.20151 0.24198 0.2513 RANDOM 23.384
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] 0.2 -0.8 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.673 r_dihedral_angle_4_deg 18.47 r_dihedral_angle_3_deg 12.442 r_dihedral_angle_1_deg 6.498 r_scangle_it 3.277 r_scbond_it 1.962 r_angle_refined_deg 1.318 r_mcangle_it 1.293 r_angle_other_deg 0.81 r_mcbond_it 0.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.673 r_dihedral_angle_4_deg 18.47 r_dihedral_angle_3_deg 12.442 r_dihedral_angle_1_deg 6.498 r_scangle_it 3.277 r_scbond_it 1.962 r_angle_refined_deg 1.318 r_mcangle_it 1.293 r_angle_other_deg 0.81 r_mcbond_it 0.689 r_mcbond_other 0.156 r_chiral_restr 0.083 r_bond_refined_d 0.012 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 2424 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 29
Software Software Software Name Purpose HKL-2000 data collection SHARP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling