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The structure of rat cytosolic PEPCK variant E89D in complex with GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QEY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 25% PEG 3350, 0.1M HEPES PH 7.4, 8MM MNCL2, 10mM GTP
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.523 α = 90 b = 119.119 β = 107.66 c = 60.894 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 100 CCD RAYONIX MX-300 2014-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 100 94.7 0.061 14.8 7.4 84925
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 61.9 0.362 5.6 2786
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2QEY 1.55 59.56 80611 4297 94.19 0.1852 0.1835 0.1924 0.2181 0.222 RANDOM 35.464
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 r_dihedral_angle_2_deg 34.893 r_dihedral_angle_4_deg 15.681 r_dihedral_angle_3_deg 12.817 r_dihedral_angle_1_deg 6.628 r_mcangle_it 3.1 r_mcbond_it 2.187 r_mcbond_other 2.186 r_angle_refined_deg 1.532 r_angle_other_deg 0.946 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.893 r_dihedral_angle_4_deg 15.681 r_dihedral_angle_3_deg 12.817 r_dihedral_angle_1_deg 6.628 r_mcangle_it 3.1 r_mcbond_it 2.187 r_mcbond_other 2.186 r_angle_refined_deg 1.532 r_angle_other_deg 0.946 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4809 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 50
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing