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The structure of rat cytosolic PEPCK variant E89Q in complex with phosphoglycolate and GDP
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 GDP
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.176 α = 90 b = 119.717 β = 107.29 c = 60.897 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 ADSC QUANTUM 315r 2011-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97 SSRL BL7-1
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 98.3 0.065 13.7 5.8 90078
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 1.61 96.4 0.411 5 8821
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 35.5 85515 4508 97.96 0.2098 0.2083 0.2162 0.2369 0.2414 RANDOM 34.592
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] 0.57 0.36 -0.74 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.097 r_dihedral_angle_4_deg 16.014 r_dihedral_angle_3_deg 13.135 r_dihedral_angle_1_deg 6.628 r_angle_refined_deg 1.775 r_mcangle_it 1.128 r_angle_other_deg 1.018 r_mcbond_it 0.664 r_mcbond_other 0.663 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.097 r_dihedral_angle_4_deg 16.014 r_dihedral_angle_3_deg 13.135 r_dihedral_angle_1_deg 6.628 r_angle_refined_deg 1.775 r_mcangle_it 1.128 r_angle_other_deg 1.018 r_mcbond_it 0.664 r_mcbond_other 0.663 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4798 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 68
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing