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apo form of XN-IL lectin from Xenorhabdus nematophila
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 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.826 α = 90 b = 76.695 β = 90 c = 148.593 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 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) 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 1.56 48.14 100 0.192 0.2 0.997 2.56 13.1 83546 14.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.64 99.9 1.164 0.773 2.8 13.1
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 1.56 48.137 83447 4396 99.907 0.172 0.171 0.1826 0.1965 0.2042 15.127
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] -0.276 -0.289 0.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.378 r_dihedral_angle_4_deg 27.384 r_dihedral_angle_3_deg 10.139 r_dihedral_angle_1_deg 6.912 r_lrange_it 4.977 r_lrange_other 4.824 r_scangle_it 3.612 r_scangle_other 3.611 r_scbond_it 2.427 r_scbond_other 2.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.378 r_dihedral_angle_4_deg 27.384 r_dihedral_angle_3_deg 10.139 r_dihedral_angle_1_deg 6.912 r_lrange_it 4.977 r_lrange_other 4.824 r_scangle_it 3.612 r_scangle_other 3.611 r_scbond_it 2.427 r_scbond_other 2.426 r_mcangle_other 2.002 r_mcangle_it 2 r_angle_refined_deg 1.728 r_angle_other_deg 1.474 r_mcbond_it 1.365 r_mcbond_other 1.356 r_nbd_refined 0.208 r_symmetry_nbd_other 0.181 r_symmetry_xyhbond_nbd_refined 0.18 r_nbd_other 0.174 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.14 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.085 r_metal_ion_refined 0.083 r_symmetry_nbtor_other 0.082 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 3789 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling MOLREP phasing