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X-ray structure of human galectin-10 in complex with D-N-acetylgalactosamine
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 2.71 54.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.9 α = 90 b = 48.9 β = 90 c = 261.66 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 2019-08-28 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 1.93 19.63 99.8 0.998 16.8 19.3 14992
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 1.93 1.98 0.903
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1QKQ 1.93 19.628 14992 759 99.814 0.203 0.2017 0.2105 0.2332 0.2363 17.848
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] 0.001 0.001 0.001 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.522 r_dihedral_angle_4_deg 22.931 r_dihedral_angle_3_deg 17.407 r_dihedral_angle_1_deg 9.076 r_lrange_it 3.915 r_lrange_other 3.915 r_scangle_it 2.653 r_scangle_other 2.651 r_mcangle_it 1.78 r_mcangle_other 1.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.522 r_dihedral_angle_4_deg 22.931 r_dihedral_angle_3_deg 17.407 r_dihedral_angle_1_deg 9.076 r_lrange_it 3.915 r_lrange_other 3.915 r_scangle_it 2.653 r_scangle_other 2.651 r_mcangle_it 1.78 r_mcangle_other 1.779 r_scbond_it 1.635 r_scbond_other 1.634 r_angle_refined_deg 1.363 r_angle_other_deg 1.189 r_mcbond_it 1.068 r_mcbond_other 1.068 r_nbd_refined 0.17 r_symmetry_nbd_other 0.165 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.155 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.12 r_symmetry_nbd_refined 0.083 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1159 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing