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Polaromonas naphthalenivorans phosphoenolpyruvate carboxykinase in complex with beta-sulfopyruvate
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 8 293 100 mM TRIS-Cl pH 8.0, 0.4 M LiCl2, 5 mM MgCl2, 1 mM MnCl2, 30-40% PEG 8000 and 10 mM beta-sulfopyruvate. 15 mg/mL PnPEPCK
Crystal Properties Matthews coefficient Solvent content 2.46 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.784 α = 90 b = 86.097 β = 90 c = 113.423 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 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 1.71 68.6 96.1 0.172 0.179 0.05 0.998 5.7 12.6 72872 27.58
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 1.71 1.77 73.9 2.74 2.855 0.805 0.655 0.26 12.6
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 1.71 68.58 1.33 70331 3464 96.13 0.191 0.189 0.189 0.2292 0.2289 31.78
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 12.3642 f_angle_d 0.7994 f_chiral_restr 0.0511 f_bond_d 0.0067 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4745 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling MOLREP phasing