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Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with 2'-fucosyllactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 1.2 M Ammonium sulfate, 0.1 M HEPES, 4 % v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 1.95 36.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.292 α = 90 b = 129.962 β = 96.96 c = 45.207 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 2 44.96 99.7 0.125 0.052 0.996 12.3 4.9 34862
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 99.5 0.274 0.157 0.866 6.3 4 2575
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 3OJB 2 44.96 33112 1718 99.17 0.165 0.1626 0.1644 0.2128 0.2153 RANDOM 32.147
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] -9.29 0.41 9.76 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.436 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_4_deg 12.003 r_dihedral_angle_1_deg 6.821 r_mcangle_it 2.213 r_angle_refined_deg 1.4 r_mcbond_it 1.346 r_mcbond_other 1.346 r_angle_other_deg 1.202 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.436 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_4_deg 12.003 r_dihedral_angle_1_deg 6.821 r_mcangle_it 2.213 r_angle_refined_deg 1.4 r_mcbond_it 1.346 r_mcbond_other 1.346 r_angle_other_deg 1.202 r_chiral_restr 0.115 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4350 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing