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Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I8T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 3.5 M Sodium formate, 0.1 M Tris
Crystal Properties Matthews coefficient Solvent content 1.89 34.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.238 α = 90 b = 64.533 β = 90.88 c = 64.685 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 45.68 99.5 0.074 0.039 0.998 15.8 4.5 35098
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 97.4 0.279 0.149 0.943 5.2 4.3 2534
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3I8T 2 45.68 33349 1732 99.46 0.1858 0.1839 0.192 0.2219 0.2306 RANDOM 18.537
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] -0.82 -0.16 1.61 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 16.493 r_dihedral_angle_3_deg 14.507 r_dihedral_angle_1_deg 6.564 r_mcangle_it 1.845 r_angle_other_deg 1.35 r_angle_refined_deg 1.344 r_mcbond_it 1.1 r_mcbond_other 1.099 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 16.493 r_dihedral_angle_3_deg 14.507 r_dihedral_angle_1_deg 6.564 r_mcangle_it 1.845 r_angle_other_deg 1.35 r_angle_refined_deg 1.344 r_mcbond_it 1.1 r_mcbond_other 1.099 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4423 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing