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Crystal structure of a formate acetyltransferase (PFL) from Amygdalobacter indicium (CoA complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 38OD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Morpheus Fusion A5 20% (v/v) PEG 500 MME; 10 % (w/v) PEG 20000; 0.05M Sodium HEPES; 0.05M MOPS (acid) pH 7.5; 0.02M 1,6-Hexanediol; 0.02M 1-Butanol
0.02M 1,2-Propanediol; 0.02M 2-Propanol; 0.02M 1,4-Butanediol; 0.02M 1,3-Propanediol; 0.02M DL-Glutamic acid monohydrate; 0.02M DL-Alanine; 0.02M Glycine; 0.02M DL-Lysine monohydrochloride; 0.02M DL-Serine, AminA.20507.a.A1.PW39584 at 25.1 mg/mL. Cocrystallization with 5mM CoA. plate 21327 A5 drop 2. puck PSL0805, Cryo: direct
Crystal Properties Matthews coefficient Solvent content 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.526 α = 90 b = 102.526 β = 90 c = 228.971 γ = 120
Symmetry Space Group P 32 2 1
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 EIGER2 XE 9M 2026-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
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 2.15 48.11 100 0.081 0.085 0.025 0.999 15.6 11 76636
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 2.15 2.19 100 1.646 1.722 0.503 0.631 11.5
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 2.2 48.11 1.34 71603 3642 99.98 0.1868 0.1842 0.1888 0.2377 0.237
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 17.474 f_angle_d 0.851 f_chiral_restr 0.048 f_plane_restr 0.01 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9602 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 133
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction