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LecA in complex with a tolcapone derivative glycomimetic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKO tetramer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 26% Peg 6K, 1M LiCl and 100 mM sodium acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.214 α = 90 b = 81.214 β = 90 c = 165.029 γ = 90
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 2023-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
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 1.95 47.13 100 0.126 0.146 0.074 0.996 8.7 7.7 77579 27.95
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 1.95 1.99 99.9 0.723 0.852 0.442 0.798 2.3
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 1.95 47.13 77518 3915 99.977 0.168 0.1661 0.1613 0.2025 0.1988 27.369
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] -8.471 -8.471 16.943
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.948 r_dihedral_angle_6_deg 14.159 r_dihedral_angle_3_deg 12.519 r_dihedral_angle_1_deg 6.542 r_lrange_it 6.084 r_lrange_other 6.023 r_scangle_it 4.843 r_scangle_other 4.843 r_scbond_it 3.648 r_scbond_other 3.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.948 r_dihedral_angle_6_deg 14.159 r_dihedral_angle_3_deg 12.519 r_dihedral_angle_1_deg 6.542 r_lrange_it 6.084 r_lrange_other 6.023 r_scangle_it 4.843 r_scangle_other 4.843 r_scbond_it 3.648 r_scbond_other 3.648 r_mcangle_it 3.424 r_mcangle_other 3.424 r_mcbond_it 2.852 r_mcbond_other 2.852 r_angle_refined_deg 1.925 r_angle_other_deg 0.692 r_symmetry_nbd_other 0.212 r_nbd_refined 0.205 r_nbtor_refined 0.189 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.143 r_metal_ion_refined 0.119 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7196 Nucleic Acid Atoms Solvent Atoms 893 Heterogen Atoms 215
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing