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LecB from Pseudomonas aeruginosa in complex with a synthetic thiofucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A3O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293.15 PEG 8000, Tris, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.488 α = 90 b = 96.951 β = 90 c = 128.68 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 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) 0.9760 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 1.85 48.69 99.9 0.999 12 13.6 80145
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 1.85 1.95 0.753 2.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 48.69 80064 3930 99.87 0.187 0.1854 0.2194 0.2065 24.788
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] -0.89 -0.558 1.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.188 r_dihedral_angle_3_deg 10.587 r_dihedral_angle_1_deg 7.222 r_dihedral_angle_2_deg 6.037 r_lrange_it 4.912 r_lrange_other 4.912 r_scangle_it 4.251 r_scangle_other 4.251 r_scbond_it 2.828 r_scbond_other 2.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.188 r_dihedral_angle_3_deg 10.587 r_dihedral_angle_1_deg 7.222 r_dihedral_angle_2_deg 6.037 r_lrange_it 4.912 r_lrange_other 4.912 r_scangle_it 4.251 r_scangle_other 4.251 r_scbond_it 2.828 r_scbond_other 2.828 r_mcangle_it 2.473 r_mcangle_other 2.472 r_mcbond_it 1.849 r_mcbond_other 1.849 r_angle_refined_deg 1.477 r_angle_other_deg 0.541 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.202 r_symmetry_xyhbond_nbd_other 0.165 r_nbtor_refined 0.164 r_nbd_other 0.154 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.118 r_symmetry_nbtor_other 0.088 r_metal_ion_refined 0.082 r_chiral_restr 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6596 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 312
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling PHASER phasing