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Crystal structure of a sialic acid binding protein, Q216A 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
Crystal Properties Matthews coefficient Solvent content 2.16 42.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.831 α = 90 b = 61.493 β = 106.23 c = 89.394 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 2024-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.6 66.78 97.7 0.107 0.04 12.9 7.1 106140 10.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 93.7 0.509 0.188 2.2 7.1
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 1.6 66.778 106085 1989 97.671 0.181 0.1803 0.1902 0.2308 0.2413 12.969
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] 2.542 0.396 -0.719 -1.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.904 r_dihedral_angle_3_deg 12.89 r_lrange_it 10.913 r_lrange_other 9.585 r_dihedral_angle_2_deg 9.021 r_dihedral_angle_1_deg 5.812 r_scangle_it 5.651 r_scangle_other 5.614 r_mcangle_other 4.03 r_mcangle_it 4.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.904 r_dihedral_angle_3_deg 12.89 r_lrange_it 10.913 r_lrange_other 9.585 r_dihedral_angle_2_deg 9.021 r_dihedral_angle_1_deg 5.812 r_scangle_it 5.651 r_scangle_other 5.614 r_mcangle_other 4.03 r_mcangle_it 4.029 r_scbond_it 3.799 r_scbond_other 3.767 r_rigid_bond_restr 2.969 r_mcbond_it 2.736 r_mcbond_other 2.728 r_angle_refined_deg 1.538 r_angle_other_deg 0.573 r_symmetry_nbd_refined 0.245 r_nbd_other 0.226 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.185 r_xyhbond_nbd_other 0.168 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.058 r_ncsr_local_group_1 0.058 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 6229 Nucleic Acid Atoms Solvent Atoms 1130 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling REFMAC phasing