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High-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrioxamine B
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
25% PEG 550-MME
100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.7 54.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.223 α = 90 b = 76.223 β = 90 c = 102.502 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 2022-10-16 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 1.15 40.5 94.9 0.058 0.019 0.999 20.9 10.3 113334
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 1.15 1.17 76.5 0.928 0.319 0.721 2.3
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 1.15 40.5 113330 2277 94.947 0.136 0.1353 0.1444 0.1529 0.1616 13.327
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] 0.099 0.05 0.099 -0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.078 r_dihedral_angle_3_deg 12.086 r_lrange_it 9.073 r_lrange_other 8.17 r_dihedral_angle_1_deg 6.143 r_scangle_it 5.286 r_scangle_other 5.285 r_mcangle_other 3.616 r_mcangle_it 3.61 r_scbond_it 3.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.078 r_dihedral_angle_3_deg 12.086 r_lrange_it 9.073 r_lrange_other 8.17 r_dihedral_angle_1_deg 6.143 r_scangle_it 5.286 r_scangle_other 5.285 r_mcangle_other 3.616 r_mcangle_it 3.61 r_scbond_it 3.408 r_scbond_other 3.402 r_dihedral_angle_2_deg 3.179 r_mcbond_it 2.368 r_mcbond_other 2.351 r_rigid_bond_restr 2.113 r_angle_refined_deg 1.669 r_dihedral_angle_other_2_deg 1.466 r_angle_other_deg 0.527 r_symmetry_nbd_refined 0.263 r_nbd_refined 0.233 r_metal_ion_refined 0.229 r_nbd_other 0.223 r_symmetry_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.183 r_symmetry_metal_ion_refined 0.132 r_xyhbond_nbd_refined 0.113 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.061 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 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 415 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing