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Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase in complex with PEP (C2221)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM TRIS-Cl pH 8.0, 0.4 M LiCl2, 5 mM MgCl2, 1 mM MnCl2, 30-40% PEG 8000 and 10 mM PEP. 15 mg/mL PnPEPCK
Crystal Properties Matthews coefficient Solvent content 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.501 α = 90 b = 110.7 β = 90 c = 162.816 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 16M 2023-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE 7B2 0.9686 CHESS 7B2
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 1.74 81.41 100 0.075 0.078 0.022 0.999 12.3 13 69062 31.8
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 1.74 1.8 99.8 1.672 1.741 0.48 0.652 0.36 12.9
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 1.74 81.41 1.34 69039 3446 99.95 0.2036 0.202 0.2026 0.2336 0.2355 37.98
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 11.3447 f_angle_d 0.6515 f_chiral_restr 0.0448 f_plane_restr 0.0052 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4677 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling MOLREP phasing