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High-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrioxamine E bound
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 0.1 M HEPES pH 7.5
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.091 α = 90 b = 76.091 β = 90 c = 102.375 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 2022-05-27 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 1.12 40.42 99.9 0.047 0.011 0.75 18.6 18.6 128565
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 1.12 1.14 98.9 0.961 0.326 0.75 2.3 9.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8XEU 1.12 40.42 128487 2634 99.943 0.126 0.1252 0.1403 0.1571 13.919
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] 0.09 0.045 0.09 -0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.362 r_dihedral_angle_3_deg 12.236 r_lrange_it 11.102 r_lrange_other 9.801 r_dihedral_angle_1_deg 6.405 r_scangle_it 6.294 r_scangle_other 6.293 r_dihedral_angle_2_deg 4.736 r_scbond_it 4.215 r_scbond_other 4.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.362 r_dihedral_angle_3_deg 12.236 r_lrange_it 11.102 r_lrange_other 9.801 r_dihedral_angle_1_deg 6.405 r_scangle_it 6.294 r_scangle_other 6.293 r_dihedral_angle_2_deg 4.736 r_scbond_it 4.215 r_scbond_other 4.214 r_mcangle_other 4.016 r_mcangle_it 4.007 r_mcbond_it 2.693 r_mcbond_other 2.683 r_rigid_bond_restr 2.507 r_angle_refined_deg 1.637 r_angle_other_deg 0.561 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.232 r_symmetry_xyhbond_nbd_refined 0.216 r_metal_ion_refined 0.208 r_nbtor_refined 0.183 r_symmetry_nbd_other 0.182 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.135 r_symmetry_metal_ion_refined 0.101 r_symmetry_xyhbond_nbd_other 0.096 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.078 r_xyhbond_nbd_other 0.028 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 2222 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing