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Rat cytosolic PEPCK in complex with GDP and phosphoglycolic acid (293K)
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 0.1 M HEPES pH 7.5, 0.5 uL of 100 mM MnCl2, 100 mM GDP, and 18-28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.416 α = 90 b = 120.893 β = 111.52 c = 60.826 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 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 1.1271 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 2.42 120.95 99.95 0.155 0.168 0.065 0.996 4.5 6.57 23314
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 2.42 2.46 100 1.867 2.017 0.758 0.623 0.2 6.94
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 2.42 56.59 1.33 23181 1160 99.31 0.2265 0.2242 0.2239 0.271 0.2707
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 8.026 f_angle_d 0.397 f_chiral_restr 0.039 f_plane_restr 0.002 f_bond_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4867 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling MOLREP phasing