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Structure of the tetrameric inhibited form of phosphofructokinase-2 from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ABQ PDB ENTRY 2ABQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 293 0.1 M sodium acetate, 12% PEG 6000, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.822 α = 90 b = 86.834 β = 90 c = 171.308 γ = 90
Symmetry Space Group P 2 2 21
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 MAR CCD 130 mm MIRRORS 2006-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.438 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.98 20 93.8 0.075 0.075 18.6 5.8 46352 43478 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.98 2.09 90.1 0.302 0.302 4.3 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2ABQ 1.98 14.94 42925 41174 2190 95.92 0.18881 0.18637 0.185 0.23377 0.233 RANDOM 24.153
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] -0.11 0.01 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.644 r_dihedral_angle_4_deg 20.688 r_dihedral_angle_3_deg 16.136 r_dihedral_angle_1_deg 5.501 r_scangle_it 2.746 r_scbond_it 1.702 r_angle_refined_deg 1.483 r_mcangle_it 0.932 r_mcbond_it 0.546 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.644 r_dihedral_angle_4_deg 20.688 r_dihedral_angle_3_deg 16.136 r_dihedral_angle_1_deg 5.501 r_scangle_it 2.746 r_scbond_it 1.702 r_angle_refined_deg 1.483 r_mcangle_it 0.932 r_mcbond_it 0.546 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.087 r_metal_ion_refined 0.017 r_bond_refined_d 0.011 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_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 4535 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing