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Crystal structure of 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 7TGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 287 0.05M Sodium phosphate pH 7.0
0.2M Ammonium sulfate
16% PEG 4000 (under oil)
Crystal Properties Matthews coefficient Solvent content 3.58 65.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.8 α = 90 b = 237.4 β = 90 c = 329.7 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 PILATUS 6M 2021-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 2.5 49.6 99.8 0.082 0.046 0.99 12.9 4.9 169125 55.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.56 1.12 0.6 0.5 1.5 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7TGK 2.5 49.6 1.34 169109 1862 99.68 0.1892 0.1888 0.1894 0.2196 0.2205 63.4
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 8.2446 f_angle_d 0.9043 f_chiral_restr 0.0501 f_plane_restr 0.0078 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23360 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 804
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing