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Structure of Escherichia coli phosphoenolpyruvate carboxykinase with bound ATP, Mg2+, and Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 4 ul drop with 4 mg/mL protein, 1 mM ADP, 1 mM phosphoenol pyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.5), 200 mM ammonium acetate and 12% PEG 4000 was allowed to equilibrate with a 1 mL reservoir of 100 mM sodium acetate, 200 mM ammonium acetate and 31% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.17 α = 90 b = 95.68 β = 95.8 c = 46.56 γ = 90
Symmetry Space Group C 1 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 110 PIXEL RIGAKU HyPix-6000HE 2025-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.58 21.97 99.8 0.023 0.057 37.2 10.8 74588 10.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.64 99.2 0.148 0.249 6.71 8.2
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 1.58 21.95 0.1 73000 1961 97.68 0.1665 0.1659 0.1659 0.1853 0.1854 14.77
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 14.8617 f_angle_d 0.8382 f_chiral_restr 0.0552 f_plane_restr 0.0073 f_bond_d 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4129 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement CrysalisPro data reduction CrysalisPro data scaling PHENIX phasing