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Crystal structure of ferrioxamine transporter FoxA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z8A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.1 M Ammonium sulphate
0.1 M HEPES pH 7.5
0.7% n-octyl-beta-d-glucoside
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.027 α = 90 b = 94.027 β = 90 c = 178.065 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M 2023-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.22 81.43 94.8 0.107 0.11 0.028 0.998 16.1 94.8 37981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.221 2.387 59.2 1.964 2.038 0.539 0.525 14.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.22 81.43 36161 1820 83.01 0.22383 0.22217 0.2259 0.25755 0.2676 RANDOM 55.98
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] -0.29 -0.15 -0.29 0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.416 r_dihedral_angle_2_deg 15.236 r_dihedral_angle_1_deg 6.443 r_long_range_B_refined 3.29 r_long_range_B_other 3.288 r_scangle_other 1.864 r_mcangle_it 1.683 r_mcangle_other 1.683 r_angle_refined_deg 1.377 r_scbond_it 1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.416 r_dihedral_angle_2_deg 15.236 r_dihedral_angle_1_deg 6.443 r_long_range_B_refined 3.29 r_long_range_B_other 3.288 r_scangle_other 1.864 r_mcangle_it 1.683 r_mcangle_other 1.683 r_angle_refined_deg 1.377 r_scbond_it 1.171 r_scbond_other 1.131 r_mcbond_it 1.06 r_mcbond_other 1.06 r_angle_other_deg 0.479 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5514 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing