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Crystal structure of HSC-HSC-AMS bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TGM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 287 0.05M Sodium phosphate pH 7.0 0.2M Ammonium sulfate 16% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.67 66.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.643 α = 90 b = 236.822 β = 90 c = 331.096 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 PIXEL DECTRIS EIGER X 16M 2025-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97935 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.47 44.45 100 0.2674 0.99 7.66 14.1 179121 43.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.61 1.66 0.39
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 2.47 44.45 1.34 179017 9044 99.98 0.1768 0.1748 0.1756 0.2135 0.2144 55.08
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 13.6966 f_angle_d 1.139 f_chiral_restr 0.0613 f_bond_d 0.0105 f_plane_restr 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23703 Nucleic Acid Atoms Solvent Atoms 904 Heterogen Atoms 287
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing