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Crystal structure of galectin-8N in complex with LNnT
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 47.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.17 α = 90 b = 50.14 β = 90 c = 69.86 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 2 40.73 99.6 0.057 26 8.2 11695
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 2 40.73 11003 579 99.13 0.19068 0.1892 0.21679 0.2046 RANDOM 16.114
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] 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.253 r_dihedral_angle_4_deg 18.006 r_dihedral_angle_3_deg 12.262 r_long_range_B_refined 7.915 r_long_range_B_other 7.913 r_dihedral_angle_1_deg 6.875 r_scangle_other 6.488 r_scbond_it 4.38 r_scbond_other 4.378 r_mcangle_other 3.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.253 r_dihedral_angle_4_deg 18.006 r_dihedral_angle_3_deg 12.262 r_long_range_B_refined 7.915 r_long_range_B_other 7.913 r_dihedral_angle_1_deg 6.875 r_scangle_other 6.488 r_scbond_it 4.38 r_scbond_other 4.378 r_mcangle_other 3.444 r_mcangle_it 3.407 r_mcbond_it 2.421 r_mcbond_other 2.369 r_angle_refined_deg 1.393 r_angle_other_deg 0.846 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1178 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing