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XN-IL lectin from Xenorhabdus nematophila in complex with heparosan trisaccharide
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 6 278 MgSO4, MES, NaCl, ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.979 α = 90 b = 77.053 β = 90 c = 146.811 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2025-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9763 PETRA III, EMBL c/o DESY P14 (MX2)
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 1.8 49.047 99.9 0.108 0.112 0.031 0.999 13.4 13 55555 33.582
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 1.8 1.9 99.6 1.46 0.48 0.555 1.2 9.9
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 1.8 49.047 55473 2742 99.894 0.196 0.1943 0.2021 0.2375 0.2444 34.415
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] 0.202 -1.503 1.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 18.433 r_dihedral_angle_3_deg 12.546 r_dihedral_angle_1_deg 7.527 r_lrange_it 6.881 r_lrange_other 6.881 r_scangle_it 5.632 r_scangle_other 5.631 r_scbond_it 3.823 r_scbond_other 3.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.396 r_dihedral_angle_4_deg 18.433 r_dihedral_angle_3_deg 12.546 r_dihedral_angle_1_deg 7.527 r_lrange_it 6.881 r_lrange_other 6.881 r_scangle_it 5.632 r_scangle_other 5.631 r_scbond_it 3.823 r_scbond_other 3.822 r_mcangle_it 3.442 r_mcangle_other 3.442 r_mcbond_it 2.615 r_mcbond_other 2.612 r_angle_refined_deg 1.584 r_angle_other_deg 1.307 r_nbd_refined 0.2 r_symmetry_nbd_refined 0.198 r_nbd_other 0.192 r_metal_ion_refined 0.182 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.156 r_xyhbond_nbd_refined 0.137 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3832 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing