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Galectin-8 N terminal domain in complex with Methyl 3-O-[1-carboxyethyl]-beta-D-galactopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.72 54.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.777 α = 90 b = 50.145 β = 90 c = 80.695 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 298 PIXEL DECTRIS PILATUS 200K 2016-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.1 26.9 98 0.149 0.981 5.9 4.9 11077
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 95 0.782 0.546 1.9 4.8
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 FREE R-VALUE 5T7U 2.1 26.9 10508 569 97.61 0.2217 0.22009 0.234 0.25084 0.2596 RANDOM 27.404
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 31.365 r_dihedral_angle_3_deg 12.997 r_dihedral_angle_4_deg 12.531 r_long_range_B_refined 9.807 r_long_range_B_other 9.804 r_scangle_other 7.9 r_dihedral_angle_1_deg 6.539 r_scbond_it 5.438 r_scbond_other 5.432 r_mcangle_other 4.806
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.365 r_dihedral_angle_3_deg 12.997 r_dihedral_angle_4_deg 12.531 r_long_range_B_refined 9.807 r_long_range_B_other 9.804 r_scangle_other 7.9 r_dihedral_angle_1_deg 6.539 r_scbond_it 5.438 r_scbond_other 5.432 r_mcangle_other 4.806 r_mcangle_it 4.805 r_mcbond_other 3.481 r_mcbond_it 3.479 r_angle_refined_deg 1.307 r_angle_other_deg 0.829 r_chiral_restr 0.077 r_bond_refined_d 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1175 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing