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Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser complexed with ATP-Mg2+-Mn2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 A 2ul drop with 4 mg/ml protein, 20 mM Tris-HCl (pH 7.6), 0.5 mM EDTA, 5 mM ADP, 2.5 mM phosphoenolpyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 0.1 M sodium acetate, 0.05 M sodium cacodylate (pH 6.5), 15% PEG 8000 was allowed to equilibrate with a 1 ml well of 0.2 M sodium aceate, 0.1 M sodium cacodylate 30% PEG 8000. After a week a 0.1 x 0.1 x 0.4 mm crystal was removed and put in a small volume of well solution with 30% glycerol added. The crystal was put into a loop and flash cooled in liquid notrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.999 α = 90 b = 95.663 β = 96.12 c = 46.319 γ = 90
Symmetry Space Group C 1 2 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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.919 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.02 99 85.95 0.1 2.95 89783 36560 13.96
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.28 59.6 0.14 4.9 1.17
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 1AYL 2.2 18.48 24587 1282 94.1 0.15795 0.15484 0.1576 0.21792 0.1542 RANDOM 14.325
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] 0.02 -0.03 0.04 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.833 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_1_deg 5.684 r_scangle_it 2.205 r_scbond_it 1.372 r_angle_refined_deg 1.234 r_mcangle_it 0.869 r_mcbond_it 0.523 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.833 r_dihedral_angle_4_deg 16.456 r_dihedral_angle_3_deg 13.948 r_dihedral_angle_1_deg 5.684 r_scangle_it 2.205 r_scbond_it 1.372 r_angle_refined_deg 1.234 r_mcangle_it 0.869 r_mcbond_it 0.523 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.3 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.164 r_metal_ion_refined 0.107 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4133 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing