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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 6I96
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 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.515 α = 90 b = 93.515 β = 90 c = 177.817 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) 0.9763 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 2.48 80.99 93.6 0.148 0.153 0.04 0.999 13.1 14.9 16422
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 2.48 2.85 1.546 1.598 0.399 0.851
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 2.48 80.99 15576 845 50.42 0.22119 0.2187 0.2342 0.26818 0.2776 RANDOM 88.379
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] 0.72 0.36 0.72 -2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.076 r_long_range_B_other 13.741 r_long_range_B_refined 13.74 r_dihedral_angle_2_deg 10.02 r_dihedral_angle_1_deg 9.233 r_scangle_other 8.032 r_mcangle_it 6.314 r_mcangle_other 6.313 r_scbond_it 5.34 r_scbond_other 5.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.076 r_long_range_B_other 13.741 r_long_range_B_refined 13.74 r_dihedral_angle_2_deg 10.02 r_dihedral_angle_1_deg 9.233 r_scangle_other 8.032 r_mcangle_it 6.314 r_mcangle_other 6.313 r_scbond_it 5.34 r_scbond_other 5.14 r_mcbond_it 4.017 r_mcbond_other 4.017 r_angle_refined_deg 1.985 r_angle_other_deg 0.936 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 5325 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing