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LecA from Pseudomonas aeruginosa in complex with a synthetic thiogalactoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LJH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 PEG 8000, PEG 1000, magnesium chloride, Tris
Crystal Properties Matthews coefficient Solvent content 2.16 43.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.9 α = 90 b = 99.823 β = 90 c = 86.838 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 EIGER2 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) R Merge I (Observed) Rrim I (All) Rpim 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 1.7 49.91 98.3 0.136 0.147 0.057 0.992 8.5 6.7 93512
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 98.3 0.695 0.751 0.281 0.834 2.7 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 1.7 45.386 93481 4735 98.177 0.198 0.196 0.2058 0.2269 0.2339 19.113
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] 0.271 -0.174 1.105 -1.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.495 r_dihedral_angle_3_deg 10.176 r_dihedral_angle_1_deg 6.799 r_dihedral_angle_2_deg 6.526 r_lrange_it 4.226 r_lrange_other 4.226 r_scangle_it 3.342 r_scangle_other 3.341 r_mcangle_it 2.412 r_mcangle_other 2.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.495 r_dihedral_angle_3_deg 10.176 r_dihedral_angle_1_deg 6.799 r_dihedral_angle_2_deg 6.526 r_lrange_it 4.226 r_lrange_other 4.226 r_scangle_it 3.342 r_scangle_other 3.341 r_mcangle_it 2.412 r_mcangle_other 2.412 r_scbond_it 2.17 r_scbond_other 2.169 r_mcbond_it 1.658 r_mcbond_other 1.658 r_angle_refined_deg 1.564 r_angle_other_deg 0.549 r_nbd_other 0.28 r_nbd_refined 0.201 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.127 r_xyhbond_nbd_refined 0.099 r_symmetry_xyhbond_nbd_refined 0.097 r_metal_ion_refined 0.089 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7153 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling PHASER phasing