☰ Navigation Tabs
Crystal structure of a sialic acid binding protein, R113A 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 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.347 α = 90 b = 89.404 β = 90 c = 151.269 γ = 90
Symmetry Space Group P 21 21 21
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 1.7 57.74 100 0.184 0.049 8.5 13.6 92279 11.65
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 1.7 1.73 98.3 1.018 0.273 1.4 13.7
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 57.74 92170 2016 99.935 0.172 0.1715 0.1762 0.1982 0.2025 15.332
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] -1.349 -0.931 2.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.481 r_dihedral_angle_3_deg 11.968 r_dihedral_angle_2_deg 8.176 r_lrange_it 5.983 r_dihedral_angle_1_deg 5.794 r_lrange_other 5.571 r_scangle_it 4.097 r_scangle_other 4.014 r_scbond_it 2.598 r_scbond_other 2.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.481 r_dihedral_angle_3_deg 11.968 r_dihedral_angle_2_deg 8.176 r_lrange_it 5.983 r_dihedral_angle_1_deg 5.794 r_lrange_other 5.571 r_scangle_it 4.097 r_scangle_other 4.014 r_scbond_it 2.598 r_scbond_other 2.502 r_mcangle_other 1.806 r_mcangle_it 1.805 r_angle_refined_deg 1.511 r_mcbond_it 1.208 r_mcbond_other 1.206 r_angle_other_deg 0.554 r_nbd_refined 0.24 r_nbd_other 0.231 r_symmetry_nbd_refined 0.228 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.06 r_ncsr_local_group_1 0.047 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 6253 Nucleic Acid Atoms Solvent Atoms 1322 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling REFMAC phasing