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Structure of the siderophore periplasmic binding protein FtsB from Streptococcus pyogenes with ferrichrome bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 100 mM BIS-TRIS pH 6.5
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.49 α = 90 b = 62.916 β = 90 c = 67.064 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 2021-03-17 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 1.8 42.9 99.4 0.096 0.027 0.999 20.4 13 24183
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 1.8 1.84 98 0.983 0.283 0.82 3 13.6
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 3HXP 1.8 33.555 24141 1161 99.207 0.182 0.1795 0.1873 0.2265 0.2289 24.395
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] -0.634 0.733 -0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.207 r_dihedral_angle_4_deg 15.434 r_dihedral_angle_3_deg 13.825 r_dihedral_angle_1_deg 6.921 r_lrange_it 4.28 r_lrange_other 4.279 r_scangle_it 2.19 r_scangle_other 2.189 r_angle_refined_deg 1.746 r_angle_other_deg 1.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.207 r_dihedral_angle_4_deg 15.434 r_dihedral_angle_3_deg 13.825 r_dihedral_angle_1_deg 6.921 r_lrange_it 4.28 r_lrange_other 4.279 r_scangle_it 2.19 r_scangle_other 2.189 r_angle_refined_deg 1.746 r_angle_other_deg 1.427 r_scbond_it 1.364 r_scbond_other 1.364 r_mcangle_it 1.344 r_mcangle_other 1.344 r_mcbond_it 0.874 r_mcbond_other 0.87 r_symmetry_xyhbond_nbd_refined 0.23 r_nbd_other 0.228 r_symmetry_nbd_refined 0.215 r_nbd_refined 0.212 r_nbtor_refined 0.174 r_symmetry_nbd_other 0.172 r_xyhbond_nbd_refined 0.154 r_xyhbond_nbd_other 0.138 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 257 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing