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The structure of a crystallizable variant of E. coli pyruvate formate-lyase activating enzyme bound to SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 300 4 uL of protein (10 mg/mL PFL-AE-CCR8 in 12.5 mM HEPES, 200 mM KCl, 3.5 mM SAM, 5.0 mM WT 7-mer PFL peptide, and 2.5 mM DTT) with 1 uL of crystallization reservoir solution (28% PEG 3350, 100 mM glycine, pH 9.0) in hanging drop format over 50 uL of crystallization reservoir solution
Crystal Properties Matthews coefficient Solvent content 2.03 39.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.405 α = 90 b = 59.094 β = 90 c = 83.545 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M-F 2017-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 APS 24-ID-C
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 1.46 41.77 96.88 0.05246 0.056 0.01912 0.999 19.76 7.6 39365 16.31
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 1.46 1.512 91.96 0.2999 0.3205 0.1104 0.959 3.66 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.46 41.77 1.37 39365 1890 96.49 0.1522 0.1511 0.1511 0.173 0.1719 24.39
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 16.9913 f_angle_d 1.1976 f_chiral_restr 0.0834 f_plane_restr 0.0125 f_bond_d 0.0117
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1975 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling PHASER phasing