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Crystal structure of a sialic acid binding protein, R404A 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, 3.8M ammonium sulfate, pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.12 41.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.255 α = 90 b = 61.146 β = 106.127 c = 88.873 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) 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 1.797 85.376 92 0.1722 0.1858 0.0692 0.993 7.78 7.11 55625
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) 1.797 1.855 90.1 0.5931 0.6423 0.2435 0.875 3.02 6.58 2781
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 1.797 85.376 55625 2715 73.814 0.198 0.1947 0.2048 0.2525 0.2567 9.143
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] 0.534 -0.011 -0.223 -0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.136 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_2_deg 7.707 r_dihedral_angle_1_deg 6.436 r_lrange_it 4.312 r_lrange_other 3.962 r_scangle_it 2.318 r_scangle_other 2.316 r_angle_refined_deg 1.548 r_scbond_it 1.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.136 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_2_deg 7.707 r_dihedral_angle_1_deg 6.436 r_lrange_it 4.312 r_lrange_other 3.962 r_scangle_it 2.318 r_scangle_other 2.316 r_angle_refined_deg 1.548 r_scbond_it 1.416 r_scbond_other 1.412 r_mcangle_it 1.363 r_mcangle_other 1.363 r_mcbond_it 0.833 r_mcbond_other 0.831 r_angle_other_deg 0.556 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.205 r_symmetry_nbd_refined 0.194 r_symmetry_nbd_other 0.191 r_nbd_other 0.19 r_nbtor_refined 0.189 r_symmetry_xyhbond_nbd_refined 0.181 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.076 r_ncsr_local_group_1 0.063 r_symmetry_xyhbond_nbd_other 0.016 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 6248 Nucleic Acid Atoms Solvent Atoms 1013 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling REFMAC phasing