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X-ray structure of human galectin-10 in complex with D-allose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QKQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10 % (v/v) 1,4-dioxane
Crystal Properties Matthews coefficient Solvent content 2.69 54.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.9 α = 90 b = 48.9 β = 90 c = 259.68 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.92 19.61 97.7 0.999 18.7 19.9 14791
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 0.911
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1QKQ 1.92 19.607 14791 747 97.714 0.182 0.1804 0.2093 0.1989 18.009
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] 0.015 0.007 0.015 -0.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.643 r_dihedral_angle_4_deg 20.763 r_dihedral_angle_3_deg 13.495 r_dihedral_angle_1_deg 8.319 r_lrange_other 4.599 r_lrange_it 4.592 r_scangle_it 3.42 r_scangle_other 3.418 r_scbond_it 2.098 r_scbond_other 2.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.643 r_dihedral_angle_4_deg 20.763 r_dihedral_angle_3_deg 13.495 r_dihedral_angle_1_deg 8.319 r_lrange_other 4.599 r_lrange_it 4.592 r_scangle_it 3.42 r_scangle_other 3.418 r_scbond_it 2.098 r_scbond_other 2.098 r_mcangle_it 1.924 r_mcangle_other 1.923 r_angle_refined_deg 1.469 r_mcbond_it 1.228 r_mcbond_other 1.22 r_angle_other_deg 1.214 r_nbd_refined 0.179 r_nbd_other 0.173 r_symmetry_nbd_other 0.164 r_symmetry_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.094 r_symmetry_nbtor_other 0.075 r_symmetry_nbd_refined 0.072 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1130 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing