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Crystal structure of E.coli Phosphopantetheine Adenylyltransferase (PPAT/CoaD) in complex with (R)-4-(5-(difluoromethyl)-1H-imidazol-1-yl)-3,3-dimethylisochroman-1-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 1.8 M AMMONIUM SULFATE, 0.25 M POTASSIUM THIOCYANATE, 0.2 M POTASSIUM BROMIDE
Crystal Properties Matthews coefficient Solvent content 2.91 57.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.48 α = 90 b = 135.48 β = 90 c = 135.48 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker Platinum 135 2017-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.1 36.21 99.4 0.111 0.125 0.058 0.997 10.6 4.4 23975 30.09
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 2.1 2.16 99.2 0.865 0.984 0.457 0.558 4.3
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 5JBN 2.104 30.294 1.34 23970 1205 99.3 0.1732 0.1714 0.172 0.2062 0.2072 34.2467
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 17.898 f_angle_d 0.988 f_chiral_restr 0.059 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2463 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 64
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction PHENIX phasing Coot model building