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High-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XEU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 50 mM Zinc sulfate
100 mM MES pH 6.5
25% PEG400
Crystal Properties Matthews coefficient Solvent content 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.924 α = 90 b = 75.924 β = 90 c = 102.859 γ = 120
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 PILATUS3 S 2M 2022-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.11 40.5 100 0.055 0.013 1 25 18.1 132170
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.11 1.13 99.3 0.725 0.29 0.751 2.2 8.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 8XEU 1.11 40.5 132091 2607 99.958 0.131 0.131 0.1308 0.1424 0.1423 14.208
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] 0.106 0.053 0.106 -0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.338 r_dihedral_angle_3_deg 14.065 r_lrange_it 11.333 r_lrange_other 9.699 r_scangle_it 6.999 r_scangle_other 6.997 r_dihedral_angle_1_deg 5.932 r_scbond_it 4.849 r_scbond_other 4.848 r_dihedral_angle_2_deg 4.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.338 r_dihedral_angle_3_deg 14.065 r_lrange_it 11.333 r_lrange_other 9.699 r_scangle_it 6.999 r_scangle_other 6.997 r_dihedral_angle_1_deg 5.932 r_scbond_it 4.849 r_scbond_other 4.848 r_dihedral_angle_2_deg 4.8 r_mcangle_other 4.033 r_mcangle_it 4.028 r_rigid_bond_restr 2.981 r_mcbond_it 2.833 r_mcbond_other 2.823 r_angle_refined_deg 1.553 r_angle_other_deg 0.526 r_symmetry_nbd_refined 0.271 r_nbd_refined 0.232 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.182 r_metal_ion_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_metal_ion_refined 0.163 r_xyhbond_nbd_refined 0.161 r_nbd_other 0.152 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.079 r_gen_planes_refined 0.009 r_bond_refined_d 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 2222 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing