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X-ray structure of human galectin-10 in complex with D-glucose
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 2.66 53.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.65 α = 90 b = 48.65 β = 90 c = 259.23 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 2018-12-06 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 2.08 19.52 99.8 0.998 15.1 19.4 11869
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 2.08 2.13 0.903 4.1
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 2.08 19.517 11869 564 99.773 0.2 0.1987 0.2078 0.2357 0.2428 22.369
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 -0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.897 r_dihedral_angle_4_deg 20.076 r_dihedral_angle_3_deg 16.116 r_dihedral_angle_1_deg 9.395 r_lrange_it 4.742 r_lrange_other 4.568 r_scangle_it 3.321 r_scangle_other 3.32 r_scbond_it 2.105 r_scbond_other 2.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.897 r_dihedral_angle_4_deg 20.076 r_dihedral_angle_3_deg 16.116 r_dihedral_angle_1_deg 9.395 r_lrange_it 4.742 r_lrange_other 4.568 r_scangle_it 3.321 r_scangle_other 3.32 r_scbond_it 2.105 r_scbond_other 2.104 r_mcangle_it 1.965 r_mcangle_other 1.964 r_angle_refined_deg 1.539 r_mcbond_it 1.263 r_mcbond_other 1.263 r_angle_other_deg 1.159 r_nbd_refined 0.185 r_nbd_other 0.184 r_symmetry_nbd_other 0.162 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.106 r_xyhbond_nbd_refined 0.1 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.058 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 1124 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing