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LecB from PA01 in complex with synthetic beta - fucosylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 30% PEG 5KMME 0.2M AmSO4 0.1M Mes pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.22 70.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.351 α = 90 b = 80.166 β = 109.361 c = 52.406 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 9M 2023-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
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 1.55 47.5 99.7 0.048 0.06 0.036 0.998 15.5 4.7 268205
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 1.55 1.58 0.37 0.471 0.289 0.922 3.5
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 1.55 47.5 56761 2853 99.661 0.138 0.1366 0.1366 0.1682 0.168 14.11
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] -0.436 -0.353 1.217 -0.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.866 r_dihedral_angle_3_deg 10.769 r_dihedral_angle_2_deg 7.846 r_dihedral_angle_1_deg 6.655 r_lrange_it 5.715 r_lrange_other 5.388 r_scangle_it 4.537 r_scangle_other 4.511 r_scbond_it 3.162 r_scbond_other 3.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.866 r_dihedral_angle_3_deg 10.769 r_dihedral_angle_2_deg 7.846 r_dihedral_angle_1_deg 6.655 r_lrange_it 5.715 r_lrange_other 5.388 r_scangle_it 4.537 r_scangle_other 4.511 r_scbond_it 3.162 r_scbond_other 3.108 r_mcangle_it 2.325 r_mcangle_other 2.325 r_angle_refined_deg 1.834 r_mcbond_it 1.65 r_mcbond_other 1.641 r_angle_other_deg 0.679 r_nbd_refined 0.23 r_symmetry_nbd_other 0.218 r_nbd_other 0.184 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.092 r_symmetry_nbd_refined 0.071 r_metal_ion_refined 0.069 r_symmetry_xyhbond_nbd_other 0.035 r_bond_refined_d 0.014 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 3295 Nucleic Acid Atoms Solvent Atoms 577 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing