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High-resolution structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrioxamine E bound (crystal form 2)
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, SITTING DROP 293.15 100 mM BIS-TRIS pH 5.5
200 mM Magnesium choride
25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.415 α = 90 b = 70.571 β = 110.658 c = 69.073 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 PILATUS3 S 6M 2022-02-08 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 1.95 47.7 99.9 0.086 0.042 0.998 12.9 6.6 40353
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 1.95 2 0.883 0.379 0.73 2
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 1.95 47.7 40336 2075 99.864 0.194 0.1915 0.1982 0.2322 0.2372 32.228
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 -0.273 0.606 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.93 r_dihedral_angle_3_deg 14.015 r_dihedral_angle_2_deg 7.472 r_dihedral_angle_1_deg 6.778 r_lrange_it 4.69 r_lrange_other 4.68 r_scangle_it 3.513 r_scangle_other 3.512 r_scbond_it 2.179 r_scbond_other 2.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.93 r_dihedral_angle_3_deg 14.015 r_dihedral_angle_2_deg 7.472 r_dihedral_angle_1_deg 6.778 r_lrange_it 4.69 r_lrange_other 4.68 r_scangle_it 3.513 r_scangle_other 3.512 r_scbond_it 2.179 r_scbond_other 2.179 r_mcangle_it 2.092 r_mcangle_other 2.092 r_angle_refined_deg 1.574 r_mcbond_it 1.398 r_mcbond_other 1.396 r_angle_other_deg 0.533 r_nbd_other 0.223 r_nbd_refined 0.22 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.139 r_symmetry_nbd_refined 0.118 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 r_metal_ion_refined 0.068 r_xyhbond_nbd_other 0.039 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4372 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing