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Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase complexed with carbon dioxide, Mg2+, ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AYL pdb entry 1AYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 293 8 microL drops: 8 mg/ml protein concentration, 2 mM ATP, 5 mM oxalate, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate, 12% PEG 4000, 1 ml resevoir: 100 mM sodium acetate, 200 mM ammonuim acetate, 27% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.854 α = 90 b = 95.564 β = 96.3 c = 46.476 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 105 CCD ADSC QUANTUM 315 mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 1.4 75.8 99.3 0.078 9.4 3.5 105079 105079 5
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) 1.4 1.45 97.8 0.402 2.1 3.35 15056
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 pdb entry 1AYL 1.6 75.81 67499 3557 99.59 0.17573 0.17451 0.1802 0.19842 0.1987 RANDOM 14.86
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] -0.88 -0.16 0.93 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.374 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 12.188 r_dihedral_angle_1_deg 5.735 r_scangle_it 2.958 r_scbond_it 1.879 r_angle_refined_deg 1.292 r_mcangle_it 1.142 r_mcbond_it 0.722 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.374 r_dihedral_angle_4_deg 14.817 r_dihedral_angle_3_deg 12.188 r_dihedral_angle_1_deg 5.735 r_scangle_it 2.958 r_scbond_it 1.879 r_angle_refined_deg 1.292 r_mcangle_it 1.142 r_mcbond_it 0.722 r_nbtor_refined 0.308 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.167 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_refined 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 4120 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALA data scaling PHASER phasing