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Fe(II)-2-oxoglutarate-dependent pseudomonal iron uptake factor C in complex with 2,4-PDCA (Mn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9HVQ7-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 0.2 M Imidazole malate, pH 5.5
33 % v/v PEG 600
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.23 α = 90 b = 81.23 β = 90 c = 226.426 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 EIGER X 16M 2023-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
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 1.9 75.48 99.9 0.089 0.093 0.029 0.997 18.9 5.4 43944 61.26
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 1.9 1.93 98.3 0.867 0.911 0.277 0.809 1.7 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 59.75 1.98 43921 2000 99.88 0.1636 0.1626 0.1624 0.185 0.1849
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.348 f_angle_d 1.027 f_chiral_restr 0.07 f_plane_restr 0.012 f_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3712 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing