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XN-IL lectin from Xenorhabdus nematophila in complex with lactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 MgSO4, MES pH 6.5, Ethylene glycol, PEG 400
Crystal Properties Matthews coefficient Solvent content 2.62 53.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.613 α = 90 b = 140.319 β = 113.973 c = 94.634 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 PIXEL DECTRIS PILATUS3 6M 2023-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9763 BESSY 14.1
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 1.69 48.438 98.7 0.108 0.117 0.044 0.998 9.5 7 243960
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 98.2 1.963 0.726 0.403 1.1 7.1
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 1.699 48.438 243914 12294 98.601 0.195 0.1931 0.2014 0.2307 0.2376 28.731
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] -0.78 0.07 2.191 -1.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.105 r_dihedral_angle_4_deg 19.55 r_dihedral_angle_3_deg 12.683 r_dihedral_angle_1_deg 7.711 r_lrange_it 5.823 r_lrange_other 5.823 r_scangle_it 4.374 r_scangle_other 4.373 r_scbond_it 3.001 r_scbond_other 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.105 r_dihedral_angle_4_deg 19.55 r_dihedral_angle_3_deg 12.683 r_dihedral_angle_1_deg 7.711 r_lrange_it 5.823 r_lrange_other 5.823 r_scangle_it 4.374 r_scangle_other 4.373 r_scbond_it 3.001 r_scbond_other 3.001 r_mcangle_it 2.804 r_mcangle_other 2.804 r_mcbond_it 2.078 r_mcbond_other 2.076 r_angle_refined_deg 1.565 r_angle_other_deg 1.305 r_nbd_refined 0.196 r_nbd_other 0.187 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.123 r_metal_ion_refined 0.109 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15293 Nucleic Acid Atoms Solvent Atoms 1444 Heterogen Atoms 498
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling MOLREP phasing