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Structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with Bisucaberin 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 293.15 150 mM KSCN
30% PEG-MME 2000
Crystal Properties Matthews coefficient Solvent content 1.99 38.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.974 α = 90 b = 62.099 β = 90 c = 67.926 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 2022-05-27 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 2 45.8 98.6 0.075 0.021 1 25.2 13.2 17418
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 2 2.05 0.996 0.281 0.817 2.9
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 2 45.8 17386 829 98.259 0.201 0.1991 0.2057 0.234 0.2381 35.564
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] -1.529 -0.303 1.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.393 r_dihedral_angle_3_deg 14.418 r_lrange_it 6.698 r_lrange_other 6.69 r_dihedral_angle_1_deg 6.33 r_scangle_it 5.31 r_scangle_other 5.309 r_dihedral_angle_2_deg 4.682 r_mcangle_it 3.415 r_mcangle_other 3.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.393 r_dihedral_angle_3_deg 14.418 r_lrange_it 6.698 r_lrange_other 6.69 r_dihedral_angle_1_deg 6.33 r_scangle_it 5.31 r_scangle_other 5.309 r_dihedral_angle_2_deg 4.682 r_mcangle_it 3.415 r_mcangle_other 3.415 r_scbond_it 3.317 r_scbond_other 3.315 r_mcbond_it 2.388 r_mcbond_other 2.388 r_angle_refined_deg 1.529 r_angle_other_deg 0.515 r_symmetry_nbd_refined 0.266 r_nbd_refined 0.223 r_nbd_other 0.216 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.138 r_symmetry_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.067 r_metal_ion_refined 0.057 r_symmetry_xyhbond_nbd_other 0.031 r_bond_refined_d 0.006 r_gen_planes_refined 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 2183 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing