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Crystal structure of a sialic acid binding protein, F87A mutant, from Streptococcus pneumoniae bound to Neu5Ac
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 293 0.1M NaCit, 3.6M ammonium sulfate, pH 5.4, 3% glycerol
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.719 α = 90 b = 61.7 β = 106.444 c = 89.648 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 XE 16M 2025-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 67.39 99.8 0.116 0.125 0.996 9.3 6.8 92071
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 95 0.635 0.711 0.848 0.8 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 1.7 67.388 91935 1952 99.616 0.186 0.1847 0.1985 0.2287 0.2415 18.337
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] 2.444 0.462 -1.805 -0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.986 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_2_deg 8.355 r_dihedral_angle_1_deg 6.173 r_lrange_it 5.009 r_lrange_other 4.794 r_scangle_it 3.768 r_scangle_other 3.766 r_scbond_it 2.41 r_scbond_other 2.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.986 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_2_deg 8.355 r_dihedral_angle_1_deg 6.173 r_lrange_it 5.009 r_lrange_other 4.794 r_scangle_it 3.768 r_scangle_other 3.766 r_scbond_it 2.41 r_scbond_other 2.375 r_mcangle_it 1.997 r_mcangle_other 1.997 r_angle_refined_deg 1.533 r_mcbond_it 1.406 r_mcbond_other 1.406 r_angle_other_deg 0.569 r_nbd_other 0.226 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.213 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.166 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6269 Nucleic Acid Atoms Solvent Atoms 1077 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling REFMAC phasing