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Crystal structure of galectin-8N in complex with Lactose
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 2.38 48.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.61 α = 90 b = 50.4 β = 90 c = 69.73 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 1.9 40.85 100 0.059 24 8.6 13910
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3AP5 1.9 40.85 13198 670 99.97 0.15213 0.15069 0.1645 0.17962 0.1932 RANDOM 16.843
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] -0.02 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.369 r_dihedral_angle_4_deg 14.785 r_dihedral_angle_3_deg 10.789 r_long_range_B_other 8.34 r_long_range_B_refined 8.321 r_dihedral_angle_1_deg 6.619 r_scangle_other 5.672 r_scbond_it 3.646 r_scbond_other 3.595 r_mcangle_other 2.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.369 r_dihedral_angle_4_deg 14.785 r_dihedral_angle_3_deg 10.789 r_long_range_B_other 8.34 r_long_range_B_refined 8.321 r_dihedral_angle_1_deg 6.619 r_scangle_other 5.672 r_scbond_it 3.646 r_scbond_other 3.595 r_mcangle_other 2.488 r_mcangle_it 2.477 r_mcbond_it 1.857 r_mcbond_other 1.831 r_angle_refined_deg 1.254 r_angle_other_deg 0.808 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 222 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing