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LecA in complex with 2-fluoro non-carbohydrate glycomimetic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKO monomer A
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 2.01 38.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.576 α = 90 b = 50.728 β = 100.011 c = 71.689 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 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 1.85 42.1 99.9 0.08 0.098 0.057 0.998 12.4 5.5 36840 20.3
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 1.85 1.89 100 0.563 0.706 0.42 0.814 5.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 41.23 36827 1850 99.916 0.161 0.1581 0.1682 0.2042 0.2144 24.2
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] 1.217 1.719 0.085 -1.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.222 r_dihedral_angle_6_deg 14.211 r_dihedral_angle_3_deg 11.775 r_dihedral_angle_1_deg 6.705 r_lrange_it 6.602 r_lrange_other 6.565 r_scangle_it 5.797 r_scangle_other 5.796 r_scbond_it 4.156 r_scbond_other 4.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.222 r_dihedral_angle_6_deg 14.211 r_dihedral_angle_3_deg 11.775 r_dihedral_angle_1_deg 6.705 r_lrange_it 6.602 r_lrange_other 6.565 r_scangle_it 5.797 r_scangle_other 5.796 r_scbond_it 4.156 r_scbond_other 4.155 r_mcangle_it 3.823 r_mcangle_other 3.823 r_mcbond_it 3.174 r_mcbond_other 3.174 r_angle_refined_deg 1.821 r_angle_other_deg 0.637 r_symmetry_nbd_refined 0.232 r_symmetry_nbd_other 0.203 r_nbd_refined 0.202 r_nbtor_refined 0.184 r_nbd_other 0.157 r_xyhbond_nbd_refined 0.143 r_ncsr_local_group_3 0.124 r_ncsr_local_group_6 0.12 r_metal_ion_refined 0.112 r_ncsr_local_group_5 0.111 r_symmetry_xyhbond_nbd_refined 0.11 r_ncsr_local_group_1 0.109 r_chiral_restr 0.102 r_ncsr_local_group_4 0.098 r_symmetry_nbtor_other 0.093 r_ncsr_local_group_2 0.093 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 3593 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing