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Crystal structure of the human galectin-4 C-terminal carbohydrate recognition domain in complex with lacto-N-neotetraose (LNnT)
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 1.9 35.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.083 α = 90 b = 127.64 β = 96.05 c = 45.102 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 2.1 44.85 99.8 0.094 0.038 0.996 19.5 5.6 29532
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 2.1 2.16 99.8 0.139 0.08 0.959 14.6 4 2449
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 2.1 44.85 28099 1403 99.82 0.2082 0.2055 0.2097 0.2654 0.2652 RANDOM 25.471
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] -0.61 0.07 1.26 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.731 r_dihedral_angle_3_deg 15.38 r_dihedral_angle_4_deg 11.174 r_dihedral_angle_1_deg 6.868 r_mcangle_it 2.228 r_angle_refined_deg 1.355 r_mcbond_it 1.283 r_mcbond_other 1.281 r_angle_other_deg 0.873 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.731 r_dihedral_angle_3_deg 15.38 r_dihedral_angle_4_deg 11.174 r_dihedral_angle_1_deg 6.868 r_mcangle_it 2.228 r_angle_refined_deg 1.355 r_mcbond_it 1.283 r_mcbond_other 1.281 r_angle_other_deg 0.873 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 142 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing