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Rat cytosolic PEPCK in complex with GTP and beta-sulfopyruvate (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, 10 mM GTP, and 18-28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.903 α = 90 b = 120.204 β = 111.49 c = 60.984 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 313 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 2.4 120.13 99.94 0.143 1.67 0.089 0.985 4 3.42 23400
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 2.4 2.44 99.92 0.903 1.093 0.609 0.606 0.8 3.06
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 2.4 60.1 1.34 23317 1082 99.48 0.2006 0.1994 0.1993 0.225 0.2254
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 12.535 f_angle_d 0.506 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4869 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling MOLREP phasing