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The crystal structure of phosphofructokinase from Lactobacillus delbrueckii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M Tris pH 7.5, 1 mM DTT, 1 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.014 α = 90 b = 135.014 β = 90 c = 77.66 γ = 120
Symmetry Space Group P 62 2 2
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-ID-B 1.0 APS 14-ID-B
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 1.85 20 98.5 0.057 0.057 50.6 18 33708
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 20 33708 1780 98.55 0.22365 0.22215 0.2226 0.25132 0.2526 RANDOM 41.108
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] -0.82 -0.41 -0.82 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.385 r_dihedral_angle_3_deg 15.849 r_dihedral_angle_4_deg 14.623 r_dihedral_angle_1_deg 5.102 r_scangle_it 2.3 r_scbond_it 1.493 r_mcangle_it 1.072 r_angle_refined_deg 1.07 r_mcbond_it 0.621 r_symmetry_vdw_refined 0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.385 r_dihedral_angle_3_deg 15.849 r_dihedral_angle_4_deg 14.623 r_dihedral_angle_1_deg 5.102 r_scangle_it 2.3 r_scbond_it 1.493 r_mcangle_it 1.072 r_angle_refined_deg 1.07 r_mcbond_it 0.621 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.117 r_symmetry_hbond_refined 0.109 r_chiral_restr 0.077 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_refined 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 2387 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing