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High-resolution structure of the siderophore periplasmic binding protein FtsB mutant Y137A from Streptococcus pyogenes
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
100 mM MES pH 6.5
25% PEG MME-550
Crystal Properties Matthews coefficient Solvent content 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.847 α = 90 b = 75.847 β = 90 c = 102.622 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 2022-03-23 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 1.15 40.4 100 0.062 0.014 1 24.6 19.4 118354
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 1.19 0.341 0.732 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.15 40.4 118277 2410 99.996 0.1314 0.1311 0.131 0.1468 0.1469 14.173
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] 0.06 0.03 0.06 -0.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.013 r_dihedral_angle_3_deg 12.444 r_lrange_it 10.667 r_lrange_other 9.615 r_scangle_it 6.848 r_scangle_other 6.782 r_dihedral_angle_1_deg 5.772 r_scbond_it 4.626 r_scbond_other 4.57 r_dihedral_angle_2_deg 4.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.013 r_dihedral_angle_3_deg 12.444 r_lrange_it 10.667 r_lrange_other 9.615 r_scangle_it 6.848 r_scangle_other 6.782 r_dihedral_angle_1_deg 5.772 r_scbond_it 4.626 r_scbond_other 4.57 r_dihedral_angle_2_deg 4.36 r_mcangle_other 4.061 r_mcangle_it 4.057 r_rigid_bond_restr 2.926 r_mcbond_it 2.769 r_mcbond_other 2.762 r_angle_refined_deg 1.623 r_angle_other_deg 0.566 r_symmetry_nbd_refined 0.355 r_nbd_other 0.274 r_nbd_refined 0.232 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.18 r_metal_ion_refined 0.149 r_xyhbond_nbd_refined 0.122 r_symmetry_xyhbond_nbd_refined 0.114 r_chiral_restr 0.087 r_symmetry_metal_ion_refined 0.086 r_symmetry_nbtor_other 0.078 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2215 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing