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Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with Blood group B trisaccharide
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 4.4 293.15 PEG1500, trisodium citrate
Crystal Properties Matthews coefficient Solvent content 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.823 α = 90 b = 81.823 β = 90 c = 112.777 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 PILATUS3 6M 2023-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.97625 BESSY 14.1
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 1.5 46.474 100 1 25.5 13.7 61937
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 1.5 1.58 100 0.847 2.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.5 46.474 61857 3147 99.992 0.176 0.1743 0.1745 0.1989 0.1994 20.274
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] 0.319 0.319 -0.638
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.208 r_dihedral_angle_3_deg 11.297 r_dihedral_angle_2_deg 9.126 r_dihedral_angle_1_deg 6.929 r_lrange_it 5.279 r_lrange_other 5.278 r_scangle_it 4.276 r_scangle_other 4.275 r_scbond_it 2.993 r_scbond_other 2.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.208 r_dihedral_angle_3_deg 11.297 r_dihedral_angle_2_deg 9.126 r_dihedral_angle_1_deg 6.929 r_lrange_it 5.279 r_lrange_other 5.278 r_scangle_it 4.276 r_scangle_other 4.275 r_scbond_it 2.993 r_scbond_other 2.992 r_mcangle_it 2.689 r_mcangle_other 2.689 r_mcbond_it 1.954 r_mcbond_other 1.943 r_angle_refined_deg 1.766 r_symmetry_xyhbond_nbd_refined 0.616 r_angle_other_deg 0.596 r_symmetry_nbd_refined 0.395 r_nbd_other 0.229 r_nbd_refined 0.199 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.088 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 3020 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing