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X-ray structure of human galectin-10 in complex with L-fucose
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 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.82 α = 90 b = 48.82 β = 90 c = 261.03 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 2018-10-05 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 1.8 19.55 99.5 0.997 15.1 18.6 18129
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 1.8 1.85 0.977
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 1.802 19.546 18129 926 99.544 0.215 0.2126 0.2208 0.2553 0.2596 16.868
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] 0.046 0.023 0.046 -0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.19 r_dihedral_angle_4_deg 19.101 r_dihedral_angle_3_deg 14.607 r_dihedral_angle_1_deg 9.106 r_lrange_it 3.625 r_lrange_other 3.617 r_scangle_it 2.396 r_scangle_other 2.394 r_mcangle_it 1.595 r_mcangle_other 1.594
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.19 r_dihedral_angle_4_deg 19.101 r_dihedral_angle_3_deg 14.607 r_dihedral_angle_1_deg 9.106 r_lrange_it 3.625 r_lrange_other 3.617 r_scangle_it 2.396 r_scangle_other 2.394 r_mcangle_it 1.595 r_mcangle_other 1.594 r_scbond_it 1.484 r_scbond_other 1.483 r_angle_refined_deg 1.419 r_angle_other_deg 1.21 r_mcbond_it 0.982 r_mcbond_other 0.982 r_nbd_refined 0.171 r_symmetry_nbd_other 0.162 r_nbtor_refined 0.16 r_nbd_other 0.157 r_symmetry_xyhbond_nbd_refined 0.151 r_xyhbond_nbd_refined 0.128 r_symmetry_nbd_refined 0.098 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.072 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 74 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing