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Structure of the 4'-phosphopantetheinyl transferase PptAb from Mycobacterium abscessus in complex with Coenzyme A and compound 153786 from the NCI Open Database
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) PEG8K
1 nmol NCI-P62 (dry compound)
Crystal Properties Matthews coefficient Solvent content 2.89 57.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.838 α = 90 b = 83.318 β = 90 c = 56.092 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 2018-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
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 1.38 46.53 99 0.065 0.068 0.998 8 3.3 115854 22.29
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 1.38 1.48 99.5 1.684 2.017 0.393 0.63 3.2
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 1.38 46.53 1.26 114843 5833 98.12 0.1699 0.1685 0.1948 0.2104 31.53
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 12.4312 f_angle_d 1.3971 f_chiral_restr 0.1049 f_bond_d 0.0125 f_plane_restr 0.0095
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1670 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 52
Software Software Software Name Purpose BUSTER refinement PHENIX refinement XDS data processing DIMPLE phasing Coot model building XSCALE data reduction XSCALE data scaling