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Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with B Lewis b pentasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other apoPLTL model, which is released together with this sctructure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 293.15 trisodium citrate, PEG1500
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.303 α = 90 b = 166.979 β = 106.629 c = 50.346 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 EIGER X 16M 2023-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97630 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.3 48.24 96.2 0.99 12.6 7.1 186694
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 0.693 2
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 1.3 46.388 186602 9353 96.066 0.144 0.1421 0.1501 0.1731 0.18 16.149
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] 1.047 -0.261 -0.297 -0.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.342 r_dihedral_angle_3_deg 11.816 r_lrange_it 11.506 r_lrange_other 11.505 r_scangle_it 8.562 r_scangle_other 8.561 r_dihedral_angle_2_deg 7.689 r_dihedral_angle_1_deg 7.101 r_mcangle_other 6.772 r_mcangle_it 6.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.342 r_dihedral_angle_3_deg 11.816 r_lrange_it 11.506 r_lrange_other 11.505 r_scangle_it 8.562 r_scangle_other 8.561 r_dihedral_angle_2_deg 7.689 r_dihedral_angle_1_deg 7.101 r_mcangle_other 6.772 r_mcangle_it 6.769 r_scbond_it 6.147 r_scbond_other 6.146 r_mcbond_it 4.834 r_mcbond_other 4.825 r_rigid_bond_restr 3.566 r_angle_refined_deg 1.697 r_angle_other_deg 0.599 r_nbd_refined 0.255 r_symmetry_nbd_other 0.199 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.176 r_nbd_other 0.168 r_symmetry_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.109 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.088 r_xyhbond_nbd_other 0.054 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6171 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 342
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling PHASER phasing