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X-ray structure of human galectin-10 in complex with D-mannose
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 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.83 α = 90 b = 48.83 β = 90 c = 260.94 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 2018-10-02 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 1.81 19.34 98 0.997 23.1 19.2 17615
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 1.81 1.86 0.918
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 1.81 19.338 17615 908 98.041 0.19 0.1886 0.1983 0.2222 0.2236 16.726
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] -0.004 -0.002 -0.004 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.9 r_dihedral_angle_4_deg 23.579 r_dihedral_angle_3_deg 14.198 r_dihedral_angle_1_deg 9.076 r_lrange_it 4.193 r_lrange_other 4.162 r_scangle_it 3.121 r_scangle_other 3.119 r_scbond_it 1.986 r_scbond_other 1.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.9 r_dihedral_angle_4_deg 23.579 r_dihedral_angle_3_deg 14.198 r_dihedral_angle_1_deg 9.076 r_lrange_it 4.193 r_lrange_other 4.162 r_scangle_it 3.121 r_scangle_other 3.119 r_scbond_it 1.986 r_scbond_other 1.986 r_mcangle_it 1.712 r_mcangle_other 1.711 r_angle_refined_deg 1.442 r_angle_other_deg 1.271 r_mcbond_other 1.071 r_mcbond_it 1.07 r_nbd_other 0.177 r_nbd_refined 0.175 r_symmetry_nbd_other 0.168 r_nbtor_refined 0.162 r_symmetry_nbd_refined 0.126 r_symmetry_xyhbond_nbd_refined 0.125 r_xyhbond_nbd_refined 0.092 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 85 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing