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X-ray structure of human galectin-10 in complex with D-galactose
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 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.66 α = 90 b = 48.66 β = 90 c = 259.8 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 2018-12-04 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) 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 1.97 19.53 97.1 0.999 18.1 20.1 13537
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 1.97 2.02 0.916
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 1.97 19.526 13537 668 97.095 0.196 0.195 0.2044 0.2248 0.2345 25.772
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] -0.102 -0.051 -0.102 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.879 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_4_deg 14.54 r_dihedral_angle_1_deg 9.527 r_lrange_other 5.42 r_lrange_it 5.417 r_scangle_it 3.923 r_scangle_other 3.923 r_mcangle_it 2.714 r_mcangle_other 2.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.879 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_4_deg 14.54 r_dihedral_angle_1_deg 9.527 r_lrange_other 5.42 r_lrange_it 5.417 r_scangle_it 3.923 r_scangle_other 3.923 r_mcangle_it 2.714 r_mcangle_other 2.713 r_scbond_it 2.487 r_scbond_other 2.477 r_mcbond_it 1.724 r_mcbond_other 1.719 r_angle_refined_deg 1.477 r_angle_other_deg 1.161 r_nbd_other 0.189 r_nbd_refined 0.167 r_nbtor_refined 0.161 r_symmetry_nbd_other 0.159 r_symmetry_nbd_refined 0.127 r_symmetry_xyhbond_nbd_refined 0.108 r_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.057 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 1151 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing