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Crystal structure of galectin-8N in complex with Glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.4 α = 90 b = 50.3 β = 90 c = 69.39 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 ADSC QUANTUM 210r 2015-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 40.73 100 0.046 24.3 7.8 23530
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 3AP5 1.58 40.73 22290 1188 99.94 0.11938 0.11791 0.14657 0.16 RANDOM 15.643
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.849 r_sphericity_free 31.274 r_dihedral_angle_4_deg 21.476 r_dihedral_angle_3_deg 10.782 r_sphericity_bonded 8.07 r_dihedral_angle_1_deg 6.746 r_long_range_B_refined 3.176 r_long_range_B_other 3.175 r_rigid_bond_restr 1.621 r_angle_refined_deg 1.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.849 r_sphericity_free 31.274 r_dihedral_angle_4_deg 21.476 r_dihedral_angle_3_deg 10.782 r_sphericity_bonded 8.07 r_dihedral_angle_1_deg 6.746 r_long_range_B_refined 3.176 r_long_range_B_other 3.175 r_rigid_bond_restr 1.621 r_angle_refined_deg 1.546 r_scangle_other 1.515 r_scbond_it 1.294 r_scbond_other 1.288 r_mcangle_it 1.093 r_mcangle_other 1.093 r_angle_other_deg 0.883 r_mcbond_it 0.775 r_mcbond_other 0.774 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1178 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing