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Structure of the siderophore periplasmic binding protein FtsB mutant Y137A 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 293.15 100 mM KSCN
30% PEG MME-550
Crystal Properties Matthews coefficient Solvent content 1.99 38.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.817 α = 90 b = 61.723 β = 90 c = 69.59 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 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 1.85 46.2 99.1 0.103 0.03 0.999 18.6 12.6 22069
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 1.85 1.89 0.851 0.292 0.729 2.4
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 1.85 46.177 22022 817 98.944 0.173 0.1714 0.1805 0.2203 0.2256 22.272
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] -1.253 0.152 1.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.556 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_1_deg 6.045 r_dihedral_angle_2_deg 4.768 r_lrange_it 4.667 r_lrange_other 4.639 r_scangle_it 3.784 r_scangle_other 3.783 r_scbond_it 2.378 r_scbond_other 2.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.556 r_dihedral_angle_3_deg 13.487 r_dihedral_angle_1_deg 6.045 r_dihedral_angle_2_deg 4.768 r_lrange_it 4.667 r_lrange_other 4.639 r_scangle_it 3.784 r_scangle_other 3.783 r_scbond_it 2.378 r_scbond_other 2.377 r_mcangle_it 1.973 r_mcangle_other 1.972 r_angle_refined_deg 1.393 r_mcbond_it 1.339 r_mcbond_other 1.337 r_angle_other_deg 0.493 r_nbd_refined 0.216 r_symmetry_nbd_other 0.186 r_nbd_other 0.179 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.135 r_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.071 r_metal_ion_refined 0.064 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2191 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing