☰ Navigation Tabs
Crystal structure of the human galectin-4 N-terminal carbohydrate recognition domain in complex with 2'-fucosyllactose
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 1.88 34.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.152 α = 90 b = 64.469 β = 90.79 c = 64.653 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 2014-07-01 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 1.85 45.65 99.1 0.041 0.024 0.998 22.9 4 44028
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 1.85 1.89 96.2 0.125 0.079 0.981 8.9 3.4 2626
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 1.85 45.65 41855 2156 98.98 0.1681 0.1662 0.1767 0.2046 0.2129 RANDOM 18.033
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] -0.86 -0.01 1.59 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.093 r_dihedral_angle_3_deg 12.141 r_dihedral_angle_4_deg 11.434 r_dihedral_angle_1_deg 6.348 r_mcangle_it 2.588 r_mcbond_it 1.757 r_mcbond_other 1.752 r_angle_refined_deg 1.105 r_angle_other_deg 0.675 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.093 r_dihedral_angle_3_deg 12.141 r_dihedral_angle_4_deg 11.434 r_dihedral_angle_1_deg 6.348 r_mcangle_it 2.588 r_mcbond_it 1.757 r_mcbond_other 1.752 r_angle_refined_deg 1.105 r_angle_other_deg 0.675 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4408 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 81
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing