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Crystal structure of a sialic acid binding protein, R113K:G213Q:Q216N mutant, from Streptococcus pneumoniae bound to Neu5Ac
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9RSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1 M Sodium citrate, pH 5
3.2 M Ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.359 α = 90 b = 61.485 β = 106.288 c = 89.296 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) R Merge I (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 2 67.033 99.9 0.27 0.292 0.109 6.2 7 55915 14.61
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 2 2.04 97.2 1.253 0.465 1.4 7.2
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 2.001 67.033 55880 1967 99.821 0.205 0.2038 0.2111 0.2443 0.2498 20.877
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] -0.17 -0.023 0.047 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.139 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 6.168 r_lrange_other 5.583 r_lrange_it 5.582 r_dihedral_angle_2_deg 5.519 r_scangle_it 4.523 r_scangle_other 4.522 r_scbond_it 2.84 r_scbond_other 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.139 r_dihedral_angle_3_deg 13.625 r_dihedral_angle_1_deg 6.168 r_lrange_other 5.583 r_lrange_it 5.582 r_dihedral_angle_2_deg 5.519 r_scangle_it 4.523 r_scangle_other 4.522 r_scbond_it 2.84 r_scbond_other 2.83 r_mcangle_it 2.433 r_mcangle_other 2.433 r_mcbond_it 1.701 r_mcbond_other 1.701 r_angle_refined_deg 1.696 r_angle_other_deg 0.586 r_symmetry_nbd_refined 0.292 r_nbd_refined 0.214 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.169 r_xyhbond_nbd_refined 0.163 r_nbd_other 0.161 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.055 r_ncsr_local_group_1 0.052 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6255 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling PHASER phasing