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XN-IL lectin from Xenorhabdus nematophila in complex with hyaluronan tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9T4Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 278 MES, ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.97 58.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.797 α = 90 b = 65.797 β = 90 c = 129.985 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS EIGER X 16M 2024-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.6888 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 43.33 99.6 0.079 0.081 0.018 0.999 19.4 20.5 43532 22.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 99.2 1.373 1.407 0.304 0.942 2.4 20.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 42.883 43510 2217 99.406 0.183 0.1817 0.1941 0.2017 0.2126 30.216
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] 1.309 0.655 1.309 -4.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.598 r_dihedral_angle_4_deg 15.008 r_dihedral_angle_3_deg 10.667 r_dihedral_angle_1_deg 7.381 r_lrange_it 5.815 r_lrange_other 5.801 r_scangle_it 4.914 r_scangle_other 4.912 r_scbond_it 3.464 r_scbond_other 3.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.598 r_dihedral_angle_4_deg 15.008 r_dihedral_angle_3_deg 10.667 r_dihedral_angle_1_deg 7.381 r_lrange_it 5.815 r_lrange_other 5.801 r_scangle_it 4.914 r_scangle_other 4.912 r_scbond_it 3.464 r_scbond_other 3.463 r_mcangle_it 2.938 r_mcangle_other 2.938 r_mcbond_other 2.256 r_mcbond_it 2.254 r_angle_refined_deg 1.82 r_angle_other_deg 1.445 r_nbd_refined 0.195 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.17 r_nbd_other 0.163 r_symmetry_nbd_refined 0.154 r_xyhbond_nbd_refined 0.122 r_metal_ion_refined 0.107 r_symmetry_xyhbond_nbd_refined 0.105 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1882 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling MOLREP phasing