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Structure of the 4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus in complex with Coenzyme A and N-(2,6-diethylphenyl)-N'-(N-ethylcarbamimidoyl)urea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 285 0.1 M LiSO4
0.1 M MES pH 6.5
20% (w/v) PEG 8K
soaking 20h in 5 mM ligand 1% DMSO
Crystal Properties Matthews coefficient Solvent content 2.88 57.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.962 α = 90 b = 83.049 β = 90 c = 56.023 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 6M 2019-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.4 46.44 98.2 0.045 0.049 0.999 15.8 6.4 57619 22.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 97.5 1.087 1.18 0.835 1.3 6.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 6QYG 1.4 46.44 1.36 57514 2908 98.21 0.1634 0.1618 0.1943 0.2062 32.19
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 12.3198 f_angle_d 1.384 f_chiral_restr 0.108 f_bond_d 0.0135 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1673 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 48
Software Software Software Name Purpose BUSTER refinement PHENIX refinement XSCALE data reduction XSCALE data scaling XDS data processing Coot model building DIMPLE phasing