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Crystal structure of AMP+PPi 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 7TGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 287 0.05M Na PO4 pH 7.0,
0.2M Ammonium sulfate,
16% PEG 4000 (under oil 100%)
Crystal Properties Matthews coefficient Solvent content 3.6 65.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.501 α = 90 b = 236.745 β = 90 c = 330.81 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 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 2.89 39.5 99.4 0.133 0.06 0.996 7.9 6.3 109861 80.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 2.94 1.5 0.71 0.6 1
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 7TGJ 2.89 39.46 1.34 109736 1988 99.35 0.1903 0.1894 0.1941 0.2354 0.235 85.28
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 9.9331 f_angle_d 1.1037 f_chiral_restr 0.0551 f_plane_restr 0.0095 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23331 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 294
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing