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Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with Lewis Y tetrasaccharide
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 4.5 293.15 PEG1500, trisodium citrate
Crystal Properties Matthews coefficient Solvent content 2.1 41.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.848 α = 90 b = 81.848 β = 90 c = 112.574 γ = 90
Symmetry Space Group P 41 21 2
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 2024-03-19 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 1.6 46.38 100 1 27.7 20 51136
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 1.6 1.69 0.888 3.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 40.958 51062 2537 99.941 0.181 0.1799 0.203 0.2015 23.069
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] 0.194 0.194 -0.387
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.121 r_dihedral_angle_3_deg 12.032 r_dihedral_angle_2_deg 9.401 r_dihedral_angle_1_deg 6.934 r_lrange_it 4.944 r_lrange_other 4.944 r_scangle_it 4.477 r_scangle_other 4.476 r_scbond_it 3.151 r_scbond_other 3.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.121 r_dihedral_angle_3_deg 12.032 r_dihedral_angle_2_deg 9.401 r_dihedral_angle_1_deg 6.934 r_lrange_it 4.944 r_lrange_other 4.944 r_scangle_it 4.477 r_scangle_other 4.476 r_scbond_it 3.151 r_scbond_other 3.15 r_mcangle_it 2.54 r_mcangle_other 2.54 r_mcbond_it 1.975 r_mcbond_other 1.973 r_angle_refined_deg 1.806 r_angle_other_deg 0.623 r_nbd_other 0.292 r_nbd_refined 0.195 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.168 r_symmetry_nbd_refined 0.144 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.095 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3052 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling PHASER phasing